This article presents comparative experimental and numerical studies to investigate the deformation and contact force of orthotropic microplates under indentation test. A simple model is developed to obtain the 3D homogenized elastic properties of orthotropic materials. In the FE simulation, the microplate is assumed to be a fully elastic orthotropic composite, and the indenter is a rigid body. Experimental indentation test is performed to obtain load-displacement curve, indentation profile, and maximum indentation depth. The numerical studies are performed to investigate the effect of indenter radius, material orthotropy, and microplate thickness on deformation of microplate under indentation load and contact pressure. The numerical model is applied to simulate two different load conditions: microplate rested on a fully supported rigid fixture, and microplate rested on a hollow support rigid fixture with circular cut-out. Numerical and experimental studies achieve excellent agreement and good correlation proving the validity of the proposed homogenization model. These parametric studies proved that the indentation behavior of orthotropic laminated structures is material independent and it depends greatly on the plate thickness.