A class of devices based on the atomic force microscope [Phys. Rev. Lett.56, 930 (1986)] is proposed that would enable imaging with tips of atomically defined structure. These molecular tip array (MTA) systems would enable sequential application of tips with differing structures to a single sample, limited to a small substrate area. MTAs with suitable binding sites can enable nanofabrication via positional chemical synthesis exploiting local effective concentration enhancements of ∼108. A method for canceling or inverting the net van der Waals attraction between a tip and a substrate in a fluid medium is suggested, and a new analysis of imaging forces for proteins is presented.