Two approaches were developed using an ambient atomic force microscope (AFM) to pattern metal in either positive or negative tone. The difference in surface chemical reactivity between exposed and unexposed regions was used to selectively attach colloidal Pd(II) nanoparticles capable of initiating the deposition of electroless (EL) Ni. In one case, EL Ni was selectively deposited in the unexposed regions of an organosilane film. In the second case, EL Ni was selectively deposited directly on an AFM oxide pattern. Based on the different binding selectivities of the Pd(II) catalysts, selective deposition on AFM patterns was attributed to the presence of a carbon residue in AFM oxide patterns formed under ambient conditions. The patterned Ni films were used as a mask for pattern transfer into the underlying substrate by reactive ion etching.