We developed the simulation model of deep Si etching for MEMS fabrication. This model includes the physical effect of ions under the presence of plasma molding, chemical etching by radicals, and the formation of a passivation layer on the wafer. The simulation was carried out in SF6/O2 in two-frequency capacitively coupled plasma using an extended vertically integrated computer aided design for device processing (VicAddress). We estimated the local characteristics of plasma structures (such as potential distribution, ion velocity distribution) near an artificial microscale hole pattern on the wafer. In this case, the sheath thickness is comparable to or even smaller than the size of the hole. Thus, the sheath tends to wrap around the hole on the wafer. The distorted sheath field directly affects the incident flux and velocity distributions of ions. The angular distribution of ions at the edge of the hole is strongly distorted from the normal incidence. The ion flux becomes radially nonuniform in the vicinity of the hole pattern. That is, the etching profile is distorted particularly at the bottom corner because of the removal of the passivation layer by energetic ion under the presence of plasma molding.