Hydrogels have many applications in biomedical surface modification and tissue engineering. However, the structuring of hydrogels after their formation represents still a major challenge, in particular due to their softness. Here, a novel approach is presented that is based on the combination of atomic force microscopy (AFM) and nanofluidics, also referred to as FluidFM technology. Its applicability is demonstrated for supramolecular hydrogel films that are prepared from low-molecular weight hydrogelators, such as derivates of 1,3,5-benzene tricarboxamides (BTAs). BTA films can be dissolved selectively by ejecting alkaline solution through the aperture of a hollow AFM-cantilever connected to a nanofluidic controller. The AFM-based force control is essential in preventing mechanical destruction of the hydrogels. The resulting "chemical writing" process is studied in detail and the influence of various parameters, such as applied pressure and time, is validated. It is demonstrated that the achievable structuring precision is primarily limited by diffusion and the aperture dimensions. Recently, various additive techniques have been presented to pattern hydrogels. The here-presented subtractive approach can not only be applied to structure hydrogels from the large class of reversibly formed gels with superior resolution but would also allow for the selective loading of the hydrogels with active substances or nanoparticles.