Shadow-effect compensated fabrication of magnetic tunnel junction (MTJ) semiconductor elements is disclosed. Providing shadow-effect compensated fabrication of MTJ elements can provide reduced free layer sizing for enhanced MTJ operational margin. In certain aspects, to reduce size of a free layer during fabrication of an MTJ to provide enhanced write and retention symmetry, ion beam etching (IBE) fabrication process is employed to fabricate a free layer smaller than the pinned layer. To avoid asymmetrical footing being fabricated in free layer due to shadow-effect of neighboring MTJs, an ion beam directed at the MTJ is shadow-effect compensated. The angle of incidence of the ion beam directed at the MTJ is varied as the MTJ is rotated to be less steep when another MTJ is in directional line of the ion beam and the MTJ being fabricated. Thus, the free layer is etched more uniformly in the MTJ while avoiding increased etching damage.