Methods and apparatus are disclosed for performing charged-particle-beam (CPB) microlithography, in which states of contamination of any of various components in the CPB column are monitored. From data concerning state(s) of contamination of one or more components, information is provided regarding when system cleaning is required (i.e., cleaning intervals). Thus, problems such as degradation of resolution and increased beam deflection distortion over time are avoided, and consistently more accurate pattern transfers are performed. Detection of contaminants on selected component(s) can be performed by mass analysis of contaminant molecules released from the component(s) during irradiation of the component(s) with the charged particle beam. Mass analysis data are routed to a control computer, which analyzes a correlation between the types and amounts of molecules of a specific contaminant and detected beam-position variance arising from accumulated contaminant. From the correlation, the control computer predicts an optimal schedule for performing maintenance activities of the component(s), such as cleaning or component replacement.