Helium ion microscopy has attracted many applications in imaging, nanofabrication and analysis. One important field of study in nanofabrication using ion beam is the milling or etching of materials using a helium or neon focused ion beam (FIB), with and without chemical gas assistance. In particular, the neon FIB has a relatively high sputtering rate with a lower probability of swelling and less re-deposition issues compared to a helium FIB. Here, both neon and helium FIB etchings are investigated for milling and repairing electron-beam lithography (EBL) defined hydrogen silsesquioxane (HSQ) and polymethyl methacrylate (PMMA) resist patterns. Different dosages of neon FIB etching result in distinct etching profiles. Using the appropriate doses, arrays of uniform gap with aspect ratio more than 20 can be achieved on HSQ nanostructures. The neon FIB etching has a resolution of 20 nm on HSQ patterns. With XeF2 assistance, neon FIB etching can be enhanced for etching depth by a factor of ∼1.2. Whereas, helium FIB can also etch thick HSQ patterns, with much lower etch rates. But with XeF2 assistance, helium FIB etching depth can be enhanced significantly by a factor of around 5. Furthermore, both helium and neon FIB etching methods have been employed to selectively remove residual particles in deep and narrow trenches without affecting the resist patterns. The chemical analysis of these residual particle composition and resist patterns can be also performed using helium ion microscopy coupled with secondary ion mass spectrometry (SIMS) using neon FIB. Besides, a neon FIB can also effectively etch PMMA patterns which are commonly used in nanofabrication and the unwanted connections can be etched away.