Medical femtosecond laser devices are used in dermatology for non-linear high-resolution imaging to obtain non-invasive and label-free optical skin biopsies (multiphoton tomography) as well as in ophthalmology for refractive corneal surgery and cataract surgery. Applications of commercial certified multiphoton tomographs include early detection of skin cancer within minutes by two-photon autofluorescence imaging of coenzymes and melanin and second harmonic imaging of collagen as well as by testing the efficacy of pharmaceutical and cosmetical products. Goals are (i) to reduce the number of physically taken human skin biopsies in hospitals and research institutions, (ii) to optimize personalized medicine, and (iii) to reduce animal studies in pharmacy. Current diagnostic tools in dermatology include surface microscopy with a dermatoscope and ultrasound but have poor resolution. Optical coherence tomography and confocal reflectance microscopy have better resolution but provide limited information based on changes of the intratissue refractive index. Multiphoton tomography provides the best resolution of all clinical imaging methods and offer functional imaging such as optical metabolic imaging based on autofluorescence lifetime imaging. Goals of femtosecond laser eye treatment are (i) the replacement of mechanical microkeratomes for corneal flap generation, (ii) the replacement of the UV nanosecond excimer laser for stroma removal, and (iii) to replace, in part, the scalpel in the surgery of cataracts and other eye diseases. So far, millions of eye treatments have been conducted around the world. The major disadvantage of current certified medical femtosecond laser devices is the high price compared with the standard mechanical and optical medical devices.