Scanning probe lithography (SPL) is a promising candidate approach for desktop nanofabrication, but trade-offs in throughput, cost, and resolution have limited its application. The recent development of cantilever-free scanning probe arrays has allowed researchers to define nanoscale patterns in a low-cost and high-resolution format, but with the limitation that these are duplication tools where each probe in the array creates a copy of a single pattern. Here, we report a cantilever-free SPL architecture that can generate 100 nanometer-scale molecular features using a 2D array of independently actuated probes. To physically actuate a probe, local heating is used to thermally expand the elastomeric film beneath a single probe, bringing it into contact with the patterning surface. Not only is this architecture simple and scalable, but it addresses fundamental limitations of 2D SPL by allowing one to compensate for unavoidable imperfections in the system. This cantilever-free dot-matrix nanoprinting will enable the construction of surfaces with chemical functionality that is tuned across the nano- and macroscales.