Vertical microscale holes in Si(100) substrate were formed using a wet chemical method, metal-assisted chemical etching (MacEtch), with patterned Au catalyst films. Three types of samples were prepared for the MacEtch process: Au/Si, Au/SiO2/Si and Au/Ti/Si. To obtain well-defined holes in the Si substrate, the usefulness of an interlayer between the metal catalyst and the Si substrate was demonstrated. Here, the effect of the interlayer is discussed. The suppression of interdiffusion between the catalyst Au and the Si substrate by the interlayer was important to maintain the shape of the patterned catalyst layers, which influenced the morphology of the etched Si.