Detailed 3D imaging of Gas Electron Multiplier (GEM) foil hole geometry was realized. Scanning White Light Interferometry was used to examine six topological parameters of GEM foil holes from both sides of the foil. To study the effect of the hole geometry on detector gain, the ANSYS and Garfield ++ software were employed to simulate the GEM detector gain on the basis of SWLI data. In particular, the effective gain in a GEM foil with equally shaped holes was studied. The real GEM foil holes exhibited a 4% lower effective gain and 6% more electrons produced near the exit electrode of the GEM foil than the design anticipated. Our results indicate that the GEM foil hole geometry affects the gain performance of GEM detectors.