We have established a dry process based on molecular beam epitaxy (MBE) of organic molecules under ultrahigh vacuum (UHV) condition on a clean and bare silicon surface. We designed a new MBE system suited to depositing organic materials based on the Monte Carlo simulation of the molecular motion. Cu phthalocyanine thin films were prepared with the system as a test. Films with high flatness and crystallinity without contamination were prepared on the substrates prepared by the UV/HF method developed earlier in our research group. The possibility of controlling the crystal structure of the deposited thin film by the surface crystallinity of the substrate is suggested based on the observation on differently prepared substrate surfaces.