Microprobe tips are commonly used to perform in-situ micromechanical tests within an electron microscope. In service, such tips have a tendency to accumulate along their surface a layer of deposited material. Tip cleanliness is crucial in order to obtain reliable and reproducible data; however, cleaning of such tips can be arduous, due to their fragility. The literature on appropriate tip cleaning methods is relatively sparse; we aim in this study to fill this gap by presenting an effective way to clean flat punch diamond microprobe tips within an electron microscope, based on mechanical scraping. Initial attempts to remove deposits from a contaminated diamond tip using two micro-brush samples, one containing silica needles and the other containing cementite lamellae, were unsuccessful, due to the adherence of the deposit to the surface of the tip and its apparently high hardness. The successful cleaning method consists of milling a silicon ridge by means of a focused ion beam, and then using this ridge to effectively scrape the deposits off the tip surface in a controlled and complete manner. This method avoids potential damage to the microprobe and can be implemented easily to clean flat punch tips rapidly within a scanning electron microscope.