This study deals with crystal orientation effect along with the effects of microstructure on the pile-ups which affect the nanoindentation measurements. Two metal classes, face centered cubic (FCC) and body centered cubic (BCC, are dealt with in the present study. The objective of this study was to find out the degree of inaccuracy induced in nanoindentation measurements by the inherent pile-ups and sink-ins. Also, it was the intention to find out how the formation of pile-ups is dependant upon the crystal structure and orientation of the plane of indentation. Nanoindentation, Nanovision, scanning electron microscopy, electron dispersive spectroscopy and electron backscattered diffraction techniques were used to determine the sample composition and crystal orientation. Surface topographical features like indentation pile-ups and sink-ins were measured and the effect of crystal orientation on them was studied. The results show that pile-up formation is not a random phenomenon, but is quite characteristic of the material. It depends on the type of stress imposed by a specific indenter, the depth of penetration, the microstructure and orientation of the plane of indentation. Pile-ups are formed along specific directions on a plane and this formation as well as the pile-up height and the contact radii with the indenter is dependant on the aforesaid parameters. These pile-ups affect the mechanical properties like elastic modulus and hardness measurements which are pivotal variables for specific applications in micro and nano scale devices.