The highly energetic electron beam (e-beam) in a scanning transmission electron microscope (STEM) can induce local changes in the state of matter, ranging from knock-on and atomic movement, to amorphization/crystallization, and to localized chemical/electrochemical reactions. To date, fundamental studies of e-beam induced phenomena and practical applications have been limited by conventional STEM e-beam rastering modes that allow only for uniform e-beam exposures. Here, an automated liquid phase nanolithography method has been developed that enables the direct writing of nanometer scaled features within microfabricated liquid cells. An external e-beam control system, connected to the scan coils of an aberration-corrected STEM, is used to precisely control the position, dwell time, and scan rate of a sub-nanometer STEM probe. Site-specific locations in a sealed liquid cell containing an aqueous solution of H2PdCl4 are irradiated to deposit palladium nanocrystals onto silicon nitride membranes in a highly controlled manner. The threshold electron dose required for the radiolytic deposition of metallic palladium has been determined, the influence of electron dose on the nanolithographically patterned feature size and morphology is explored, and a feedback-controlled monitoring method for active control of the nanofabricated structures through STEM detector signal monitoring is proposed. This approach enables fundamental studies of electron beam induced interactions with matter in liquid cells and opens new pathways to fabricate nanostructures with tailored architectures and chemistries via shape-controlled nanolithographic patterning from liquid-phase precursors.