Electrochemically manufactured mesoporous silicon layers are widely used in the sensor or microfluidic technology especially for analysis of nano substances. Surface functionalization and pore filling of mesoporous layers are essential key aspects for successful application of complex porous matrices. Atomic layer deposition offers a possibility for the appropriate functionalization or pore filling with well-controlled process parameters at the nanoscale level. In these experiments mesoporous silicon layers with average pore size radius of 4.68 nm and porosity of 48% were fabricated and covered with different ALD single layers, such as thermal Al2O3, plasma TiO2, thermal ZnO, and layer combinations as multilayer ALD, such as plasma Al2O3/TiO2. This contribution gives an extensive investigation of single and multilayer depositions on and into mesoporous silicon layers and analyzes the material distribution and penetration profile of the corresponding atomic compositions.