The primary cortical cells were selected as a model to study the adherence and neural network development on chemically roughened silicon substrates without any coatings using confocal laser scanning microscopy (CLSM) and atomic force microscopy (AFM). The silicon substrates have a nano-range roughness (RMS) achieved by chemical etching using hydrofluoric (HF) acid. After 7 days of culturing, the neurons were observed to connect together and form dense neural networks. Furthermore, AFM results revealed that some porous structures at a few micrometer range existed between the neuron cells and the silicon substrates. It is suggested that the porous structures are made of extracellular matrix (ECM) components and play an important role in the neuronal adhesion and neurite outgrowth on the inert silicon wafers.