Amorphous silicon (α-Si) was deposited on glass substrates by PECVD at different deposition conditions in order to characterize the residual stress on the film. Subsequently, a thermal-annealing was applied for different times at 400 °C in a N2 atmosphere, aiming to reduce the stress in the films. The deposition power was between 15 and 30 W at 13.56 MHz, the pressure in the chamber was adjusted in a range from 600 to 900 mTorr, and the temperature was varied from 140 to 200 °C. The stress was determined by using the Stoney equation, measuring the curvature and thickness of the α-Si films with a stylus profilometer. A deposition rate between 7-24 nm/min was obtained, and the time for thermal-annealing needed to reduce the stress was reduced from 10 to 2-4 h, obtaining a minimum compressive stress of 17 MPa. With this value of stress, it was possible to use the α-Si as masking material for wet etching of glass during the manufacturing of microfluidic devices, in order to obtain microstructures in the glass with 150 μm in depth.