A novel supercritical cleaning process was proposed for removing contamination in high aspect ratio trenches and microholes of highly integrated semiconductor devices. The supercritical CO2-pulse cleaning with the periodic pressure swing of supercritical fluid between subcritical and supercritical conditions was conducted for removing particles in microholes of fabricated model structures. The microhole depth is 2.0 μm with microhole sizes ranging from 0.2 μm to 1.6 μm. The effects of microhole size on particle removal were investigated by means of non-destructive observation of high aspect ratio model structures with an optical microscope and SEM. The supercritical CO2-pulse cleaning efficiently removed more than 50 nm fine particles from the deep microholes owing to its drastic changes in density near the critical point by depressurization of the supercritical fluid.