Every medical laser application is based upon the compromise between efficiency and collateral adverse effects.The optimizing strategies of preclinical investigations of IR lasers can be dramatically improved by using FEL technology, allowing the free combination of wavelength, pulselength and energy. The new approach is illustrated by the results from photoablation of three different types of tissue (cornea, dental hard substances and atheromatous plaques). FEL technology enables the optimizing of physical and biological parameters and reducing risks while minimizing time and costs involved.