Electron irradiation of self-assembled monolayers (SAMs) is a versatile tool for lithographic methods and the formation of new 2D materials such as carbon nanomembranes (CNMs). While the interaction between the electron beam and standard thiolate SAMs has been well studied, the effect of electron irradiation for chemically and thermally ultrastable N-heterocyclic carbenes (NHCs) remains unknown. Here we analyze electron irradiation of NHC SAMs featuring different numbers of benzene moieties and different sizes of the nitrogen side groups to modify their structure. Our results provide design rules to optimize NHC SAMs for effective electron-beam modification that includes the formation of sulfur-free CNMs, which are more suitable for ultrafiltration applications. Considering that NHC monolayers exhibit up to 100 times higher stability of their bonding with the metal substrate toward electron-irradiation compared to standard SAMs, they offer a new alternative for chemical lithography where structural modification of SAMs should be limited to the functional group.