Laser removal of fingerprints from glass and quartz surfaces was studied using laser irradiation in air. The KrF excimer laser, continuous wave (CW) CO2 laser and pulsed CO2 laser were used in the investigation. Electron probe microanalysis (EPMA) was performed to characterize the substrate surfaces before and after laser cleaning. It is found that short wavelength and pulse width are necessary for fingerprint removal. EPMA measurements show that KrF excimer laser irradiation can effectively remove fingerprints from glass and quartz surfaces with a few pulses if the pulse energy density is sufficiently high. In the laser removal of fingerprints from quartz surfaces, it is found that the irradiation direction of the incident laser pulse can cause significant differences in the cleaning effect for laser irradiations from the front or back. CO2 laser irradiation, either in CW or pulse form, cannot effectively remove fingerprints.