The design of the data acquisition system for the National Accelerator Centre's nuclear microprobe is described. The system consists of an intelligent PC scanner and imaging terminal, interfaced to a VAX-11/750 running a general purpose data acquisition package XSYS. In this way, the user friendliness of a dedicated, intelligent scanner has been combined with the flexibility of a general purpose data acquisition package. It is illustrated how simple tasks such as beam focussing, area of interest localization, and quantitative single spot PIYE or RBS analysis can be performed with minimal complexity, whereas requirements of a more complex nature can be implemented routinely using the general purpose acquisition package with standard command files. Even unique studies can be performed by means of minor software modifications.