Porous silicon (PS) layer was produced by photochemical etching process at (5, 7, 10, 12 and 15) etching time and 7 mA/cm2 current density then after investigation by Atomic Force Microscope (AFM) the thickness of PS layer from about 3.4 µm to 15.8 µm was determined. The surface of porous silicon is formed from small pyramids with porous structure, where the porosity of n-PS is from ≈ (32-72%). Porous silicon layer formed on the silicon substrates by photochemical etching contains also the nanopores with diameter about (16.41-42) nm in current density (7mA/cm2). The porosity and thickness was determined from AFM results and compared with the result from the usually measured porosity and thickness through a gravimetric method we found that the values of porosity and thickness calculated from two methods are approximately similar to each other with few difference, the influence of structure changes on optical properties such as refractive index, which decreases exponentially with porosity.