Fabrication of patterns on silicon and gold via Dip-Pen Nanolithography (DPN) using silica sol as ink and the combination of DPN, soft lithography, and silica sol-gel to transfer patterns from silicon and gold to stainless steel were assessed. In addition, a comparison in terms of throughput and resolution of both protocols was performed. Optical, scanning electron and atomic force microscopy were used to characterize the patterns. Silica sol showed high resolution but low throughput when used to pattern directly on gold and silicon using DPN. The combination of DPN, silica sol-gel and soft lithography showed high throughput and resolution. The present experimental methodology was useful to create patterns on a surface and transfer them to another surface of interest, which may serve as a biomaterial surface modification model.