The search of novel tools controlling the physical and chemical properties of matter at the nanoscale is crucial for developing next-generation integrated systems, with applications ranging from computing to medicine. Here, we show that thermal scanning probe lithography (t-SPL) can be a flexible tool for manipulating with nanoscale precision the surface properties of a wide range of specifically designed systems. In particular, we show that via t-SPL, we pattern nanoscale chemical patterns on polymeric substrates, which are then used to specifically bind extracellular matrix (ECM) proteins to the polymer surface. We demonstrate that the concentration of immobilized proteins can be controlled by varying the tip temperature, so that nanoscale protein gradients can be created. On a different system, we show that, by performing t-SPL on a thin film magnetic multilayer, in an external magnetic field, we are able to write reversibly magnetic patterns with arbitrarily oriented magnetization and tunable magnetic anisotropy. This demonstrates that t-SPL represents a novel, straightforward and extremely versatile method for the nanoscale engineering of the physicalchemical properties in a wide variety of materials.