In this paper, we report on the impact of sample preparation methods on the adhesion reproducibility of thin films, considering future applications of supercritical fluid deposition (SCFD) to MEMS/NEMS with high-aspect-ratio micro- and nanostructures (HARMS/ HARNS). Our experiments revealed the importance of careful cleaning before SCFD. The Cu on the samples treated with appropriate cleaning and drying sequences could stick to the sample enduring the adhesive pull-out test. By using a silicon substrate, we confirmed that sample surface contaminations were reduced by cleaning, as observed by a decrease in the carbon peak in field emission Auger electron spectroscopy (FE-AES). At the same time, a subtle roughness increase (of 0.2 nm RMS) after a series of cleaning steps was confirmed by scanning probe microscopy (SPM/AFM) measurement. On the basis of the acquired knowledge, Cu SCFD on Si surfaces was studied. A relatively low temperature (130–150 °C) deposition condition was obtained, with which the produced Cu films exhibited high adhesion on all samples. The deposition of 100-nm-thick Cu was successfully demonstrated on the sidewalls of a Si trench with 450 nm width and 22.5 μm depth (aspect ratio of 50).