Focused ion beam (FIB) milling has enabled the development of key microstructure characterization techniques (e.g. 3D electron backscatter diffraction (EBSD), 3D scanning electron microscopy imaging, site-specific sample preparation for transmission electron microscopy, site-specific atom probe tomography), and micro-mechanical testing techniques (e.g. micro-pillar compression, micro-beam bending, in-situ TEM nanoindentation). Yet, in most milling conditions, some degree of FIB damage is introduced via material redeposition, Ga+ ion implantation or another mechanism. The level of damage and its influence vary strongly with milling conditions and materials characteristics, and cannot always be minimized. Here, a masking technique is introduced, that employs standard FIB-SEM equipment to protect specific surfaces from redeposition and ion implantation. To investigate the efficiency of this technique, high angular resolution EBSD (HR-EBSD) has been used to monitor the quality of the top surface of several micro-pillars, as they were created by milling a ringcore hole in a stress-free silicon wafer, with or without protection due to an “umbrella”. HR-EBSD provides a high-sensitivity estimation of the amount of FIB damage on the surface. Without the umbrella, EBSD patterns are severely influenced, especially within 5 µm of the milled region. With an optimized umbrella, sharp diffraction patterns are obtained near the hole, as revealed by average cross correlation factors greater than 0.9 and equivalent phantom strains of the order 2 × 10−4. Thus, the umbrella method is an efficient and versatile tool to support a variety of FIB based techniques.