Digital holography (DH) is a well-established interferometric tool in optical metrology allowing the investigation of engineered surface shapes with microscale lateral resolution and nanoscale axial precision. With the advent of charged coupled devices (CCDs) with smaller pixel sizes, high speed computers and greater pixel numbers, DH became a very feasible technology which offers new possibilities for a large variety of applications. DH presents numerous advantages such as the direct access to the phase information, numerical correction of optical aberrations and the ability of a numerical refocusing from a single hologram. Furthermore, as an interferometric method, DH offers both a nodestructive and no-contact approach to very fragile objects combined with flexibility and a high sensitivity to geometric quantities such as thicknesses and displacements. These features recommend it for the solution of many imaging and measurements problems, such as microelectro-optomechanical systems (MEMS/MEOMS) inspection and characterization. In this work, we propose to improve the performance of a DH measurement on MEMS devices, through digital filters. We have developed an automatic procedure, inserted in the hologram reconstruction process, to selectively filter the hologram spectrum. The purpose is to provide very few noisy reconstructed images, thus increasing the accuracy of the conveyed information and measures performed on images. Furthermore, improving the image quality, we aim to make this technique application as simple and as accurate as possible.