Tailored writing and specific positioning of molecules on nanostructures is a key step for creating functional materials and nano-optical devices, or interfaces for synthetic machines in various applications. We present a novel approach for the selective functionalization of patterned glass surfaces with functional probes of any nature. The presented strategy is optimized for imaging fluorophore labeled nanostructures for (single-molecule) fluorescence microscopy. The first step in the protocol is coating a glass surface, here a microscope cover slide, with a 60 nm thick diamond-like carbon film. Subsequently, the pattern is defined by either writing silicon oxide on the coating with a focused electron beam, or by etching the coating with a focused ion beam to expose the glass surface. Finally, the pattern is silanized and functionalized. We demonstrate the selective binding of organic fluorophores and imaging with high contrast, especially in total-internal-reflection mode. The presented approach is flexible and combines bottom-up assembly with high-resolution lithography on glass cover slides to precisely position and image functional molecules of any type.