This paper describes a simple procedure for patterning Si substrate using a combination of surface functionalization and microcontact printing (muCP). The Si/SiO2 surfaces were chemically modified to present self-assembled monolayer (SAMs) of siloxanes terminating in reactive carboxylic anhydride groups and then patterned with poly(ethylene imine) (PEI) by muCP. We used the patterned thin films of PEI as etch resists on Si surfaces.