Micro-mechanical systems are exquisite tools for high-resolution surface patterning. As an alternative to traditional photolithography, they can be used for local material deposition at the sub-100 nm scale. This can be either done by means of liquid dispensing though nanoprobes, or by local material deposition through miniature shadow-masks (nanostencils). The MEMS-based patterning techniques are a) scalable, b) use simple equipment, c) can be applied to all sorts of substrates including elastic, and d) are entirely additive methods. The local material-adding aspect is probably to most noteworthy in that it drastically eliminates cross-contamination and enables combinatorial approaches. Due to their small size and mass micromechanical devices have a high resonance frequency (kHz-MHz) making them immune against vibration and thermal noises and applicable for rapid interactions with features on surfaces. The cantilevers and membranes are mechanically compliant with low spring constants, which allows creating soft-contacts between probe and surface and reduce the risk to damage fragile substrates. MEMS tools can be micromachined using wafer manufacturing methods with integrated sensor and actuators enabling the conception of parallel probe arrays for high throughput. Application to soft and/or fragile surfaces makes MEMS based nanopatterning versatile and useful for application in bio/nanotechnology, surface materials science, solid-state physics, nanoelectronics/molecular electronics, spintronics. MEMS-based patterning is excellent for rapid prototyping and scalable to full wafer scale. The talk will present the current state-of-the-art of the MEMS-based nanopatterning, new mechanically re-inforced nanostencils, its application for advanced thin film methods on self-assembled monolayer for molecular electronic applications, for combinatorial material research and new types of nanoscale liquid dispensers. The talk will highlight the strength of the methods, but will also discuss the current limits and challenges ahead to make it a truly reliable nanofabrication method.