We demonstrated for the first time the versatility of the previously proposed concept of DNA nanostructure integration on MEMS [1] by selectively assembling DNA nanostructures to form a bridge over a trenched silicon. A DNA origami (30 x 150 nm) was fixed to bridge a trenches (100 nm width, 200 nm depth) utilizing the hybridization between ssDNA on the DNA origami and selectively immobilized complementary ssDNA-pattern at the edges of the etched trench. An octadecylsilane self-assembled monolayer (ODS SAM) was utilized as a masking layer for a scanning probe lithography (SPL) with better process stability than a trimethylsilyl (TMS) SAM. This result opens a way to integrate the nanomaterial components on a structured device such as MEMS by using DNA origami.