Since the invention of the laser in the 60s, the main advances in laser technologywere done in two directions; shorter pulses and higher powers. In order to achievethis purpose, many laser types are developed and always replaced with simpler,smaller, cheaper alternatives that can deliver the same or better parameters. Inthe past 20 years, ber lasers have become an important alternative that canmatch and even enhance the performance of currently used lasers while reducingthe complexity, costs and instability.Optical bers, which are the main components of ber lasers, were rst de-veloped just as a substitute for conventional cables since they offer much lessattenuation in carrying signals over long ranges. So, most of the studies werefocused on making the bers better for communication channels. After realizingthat ber lasers offer better beam qualities, which is also a vital parameter formany laser applications, researches started nding ways to use bers for lasersand they achieved this in 80s by the rst ever utilization of low-attenuation ac-tive bers. After the invention of double-clad bers, utilization of diode lasers forpumping and development of efficient rare-earth doped bers, ber lasers becamemore than just a research topic in the laboratory and began to nd use in manyapplications.The utilization of ber lasers for short (nanoseconds) and ultrashort (picosec-onds, femtoseconds) pulse generation was a difficult task for researchers. Thebiggest challenge to overcome was nonlinear effects caused by the connement ofthe beam into small volumes. By using smart designs like chirped pulse ampli-cation and highly doped lasers, pulse energies and peak powers close to solid-stateultrafast lasers can be achieved. These nonlinear effects were not just problems inthe power scalability of ber lasers, on the other hand, they were an opportunityfor new possible applications. For example, using these nonlinear effects inside bers, supercontinuum generation was demonstrated and found usage in manyareas like spectroscopy, imaging and metrology.Today, more than 50 worldwide companies sell short-pulse ber lasers for ap-plications as diverse as ophthalmology, micromachining, medical imaging andprecision metrology. Especially, ber-laser-based micromachining is routinely im-plemented in the fabrication processes for widely used consumer products. Newapplications of ber lasers are being continuously developed.Consequently, in this Ph.D. thesis study, new application areas of ber lasersare investigated. Ultrashort and short pulsed ber lasers are developed and uti-lized for biological and transparent material processing, spectroscopy and imag-ing. In the rst part of thesis study, we have demonstrated the use of a custom-built ber laser-based microscope system for nanosurgery and tissue ablationexperiments. Through the use of custom FPGA electronics acting through ber-coupled AOMs, we are able to generate custom pulse sequence. Using this system,we have made photodisruption experiments in tissue level, cellular level and sub-cellular level.In the second part of this thesis study, in collaboration with Bogazici Univer-sity, we have developed a nanosecond ber laser system that is able to generatewavelength components of 600 nm to 1300 nm, developed specically for pho-toacoustic excitation. Using this system, we have made photoacoustic signalexcitation in a ceramic sample and prepared the system for further experimentsto generate photoacoustic images from biological specimens.In the third part of thesis study, in collaboration with ODTU, the developmentof a THz-TDS system driven by a novel Yb-doped ber laser whose repetitionrate can be tuned, specically for fast scan THz measurements, is realized. Char-acterization of the built laser system is done considering the necessities for theOSCAT technique as an alternative method for fast scan THz measurements.Stability of the oscillator is examined in terms of power, spectrum and pulseduration with the changing repetition rate of the laser. Using this system THzwaveforms are generated at different wavelengths and the system is prepared forfurther research in spectroscopy.In the last part of the thesis study, a high-pulse energy femtosecond lasersystem is developed and utilized for transparent material processing. The laseroutput is coupled to a fast galvo-scanner system, and a synchronized translationstage such that very wide areas (10 cm x 10 cm) are able to be processed withvery high speed (2 m/s). Using this system, glass samples are cut, engraved and photodarkened.Keywords:Ultrashort Pulse Laser, Ultrafast Laser, Fiber Laser, Fiber Amplier,High Pulse Energy Laser, Ultrafast Material Processing, Nanosurgery, TissueAblation, Multiphoton Ablation, Photoacoustic Imaging, Supercontinuum Gen-eration, Photothermal Effects, THz Spectroscopy, Photodarkening, Glass Pro-cessing.

60'l yllarda lazerin icadndan bu yana lazer teknolojisindeki gelismeler temelolarak iki yonde ilerlemistir; daha ksa atm uretme ve daha yuksek guclereulasma. Bunu basarabilmek icin bircok farkl lazer tipi gelistirilmis ve bu lazer tip-leri her seferinde, ayn isi ya da daha iyisini yapabilen, daha basit, daha kucuk vedaha ucuz alternati erle yer degistirmistir. Son 20 ylda da ber lazerler mevcutlazer teknolojisine onemli bir alternatif olarak ortaya ckms ve mevcut parame-treleri daha da ileri goturmeyi basarrken bunu daha az sistem karmasklg,maliyeti ve kararszlg ile sunmustur.Fiber lazerlerin temelini olusturan optik berler ilk olarak yaygn olarakkullanlan kablolara alternatif olmas icin telekomunikasyon alannda, sinyalleridusuk kaypla uzun mesafelere tasyabilmesi sebebiyle kullanlmaya baslanmstr.Bu nedenle ber optik alanndaki calsmalarn cogu berleri daha etkintelekomunikasyon kanallar yapmaya yogunlasmstr. Fiberlerin yuksek kalitedelazer demeti saglayabildiginin fark edilmesi ve bu parametrenin lazerler icin deonemli olmas sebebiyle berlerin lazer alannda kullanlmas icin arastrmalaryaplmaya baslanms ve 80li yllarda ilk aktif berlerin dusuk kaypl olarakuretilmesiyle sonuclar alnmaya baslanmstr. Cift-kl berlerin uretilmesi,diyot lazerlerin aktif berleri pompalama amacl kullanlmaya baslanmas ve ver-imli nadir element katkl berlerin gelistirilmesiyle ber lazerler yalnzca labo-ratuvarda bir arastrma konusu olmaktan ckp bircok uygulama alannda kul-lanlmaya baslanmstr.Fiber lazerlerin ksa (nanosaniye) ve ultra ksa (pikosaniye ya da fem-tosaniye) atm uretmede kullanlmaya baslanmas arastrmaclar icin zorlu birgorev olmustur. En buyuk zorluk lazer demetinin icinde ilerledigi dalga klavuzuortamnda kucuk bir hacme skstrlms olan sgn dogrusal olmayan etkileresebep olmasdr. Genisletilmis atm yukseltgenmesi ve yuksek katkl berlerinvi viikullanlmas gibi zekice tasarmlarla, yalnzca kat-hal lazerlerle elde edilmesimumkun olan yuksek atm enerjilerine ve tepe guclerine ulaslmstr. Dogrusalolmayan etkiler gucun artrlabilmesi icin sorun teskil etmesinin yan sra birtaraftan da bircok yeni uygulama alan icin frsat sunmaktadr.Ornek olarak,dogrusal olmayan etkilerin ber icinde kullanm ile super tayf uretilebilmektedirve spektroskopi, goruntuleme, metroloji gibi degisik alanlarda kullanm bulmak-tadr.Gunumuzde 50den fazla sirket ksa atml ber lazer satmaktadr ve bu lazer-ler optalmolojiden, malzeme islemeye, medikal goruntulemeden hassas metrolojiuygulamalarna bircok alanda kullanlmaktadr.Ozellikle ber lazer temellimikron hassasiyetinde malzeme isleme bircok urunun uretimi icin rutin olarakkullanlmaktadr. Fiber lazerlerin yeni uygulamalar da surekli gelisim icindedir.Sonuc olarak, bu doktora tez calsmasnda ber lazerlerin yeni uygulama alan-lar arastrlmstr. Ultraksa ve ksa atml ber lazerler biyolojik malzeme isleme,saydam malzeme isleme, spektroskopi ve goruntuleme amacl olarak uygulamayaozel sekilde tasarlanms ve gerceklenmistir. Tezin ilk ksmnda ultrahzl atmlarasahip bir ber lazer mikroskopa entegre edilmis ve bu sistem ile nanocerrahive doku ykmlama deneyleri gerceklestirilmistir. Akusto-optik degistirimcilerikontrol eden FPGA temelli elektronik devre tasarmlar ile atm dizileri istegebagl olarak herhangi bir snrlama olmakszn uretilebilmistir. Bu sistem kul-lanlarak ykmlama deneyleri doku, hucre ve hucre-al seviyede denenmistir.Tez calsmasnn ikinci ksmnda BogaziciUniversitesi ile ortak olarak gelistirilennanosaniye atmlara sahip 600-1300 nm aralgnda dalgaboylarna sahip ber lzersisemi gelistirilmis ve fotoakustik goruntuleme deneyleri icin kullanma hazr halegetirilmistir. Bu sistem kullanlarak, seramik bir ornekten fotoakustik sinyaluretilmesi denenmis ve gelistirilen sistem biyolojik malzemelerden fotoakustikgoruntuleme elde etmeye hazr hale getirilmistir.Tez calsmasnn ucuncu ksmnda ODTU ile ortak bir calsma cercevesindeTHz-TDS sisteminde kullanlmak uzere ozgun bir femtosaniye atml, Yb-katkl,atm tekrar sklg kaydrlabilen ber lazer gelistirilmis ve THz olcumleri icinkullanma hazr hale getirilmistir. Gelistirilen lazer sisteminin THz ocumleriicin gerekli OSCAT teknigine uygun olup olmadg kaydrma islemi srasndakikararllg karakterize edilerek test edilmistir. Lazer salngacndan elde edilen op-tik guc, spektrum ve atm suresi degisimleri olculmustur. Bu sistem kullanlarakTHz sinyal uretimi gerceklestirilmis ve spektroskopi olcumleri icin hazrlanmstr.Tez calsmasnn son ksmnda saydam malzeme isleme amacl, yuksek atm enerjili femtosaniye atml ber lazer gelistirilmistir. Gelistirilen lazerin cksgalvo-taraycya iletilmis ve bu taraycyla senkronize hareket eden bir konumlamasistemi ile genis alanlar (10 cm x 10 cm) yuksek tarama hznda (2 m/s) taramakmumkun hale gelmistir. Bu sistem kullanlarak cam ornekler uzerinde kesme,kazma ve cam icinde karartma deneyleri yaplmstr. Anahtar sozcukler: Ultraksa Atml Lazer, Ultrahzl Lazer, Fiber Lazer, FiberYukseltec, Yuksek Atm Enerjili Lazer, Ultrahzl Malzeme_Isleme, Nanocerrahi,Doku Kesimleme, Cok-fotonlu Kesimleme, Fotoakustik Goruntuleme, SupertayfUretme, Fototermal Etkiler, THz Spektroskopisi, Fotokarartma, Cam_Isleme.