We present a simple semiconductor process to fabricate nanogap arrays for application in molecular electronics and nano-bio electronics using a combination of freestanding silicon nanowires and angle evaporation. The gap distance is modulated using the height of the silicon dioxide, the width of the Si nanowires, and the evaporation angle. In addition, we fabricate and apply the nanogap arrays in single-electron transistors using DNA-linked Au nanoparticles for the detection of DNA hybridization.