High resolution ion microbeams, usually used to perform elemental mapping, low dose targeted irradiation or ion beam lithography needs a very flexible beam control system. For this purpose, we have developed a dedicated system (called "CRionScan"), on the AIFIRA facility (Applications Interdisciplinaires des Faisceaux d'Ions en Région Aquitaine). It consists of a stand-alone real-time scanning and imaging instrument based on a Compact Reconfigurable Input/Output (Compact RIO) device from National Instruments™. It is based on a real-time controller, a Field Programmable Gate Array (FPGA), input/output modules and Ethernet connectivity. We have implemented a fast and deterministic beam scanning system interfaced with our commercial data acquisition system without any hardware development. CRionScan is built under LabVIEW™ and has been used on AIFIRA's nanobeam line since 2009 (Barberet et al., 2009, 2011) [1] and [2]. A Graphical User Interface (GUI) embedded in the Compact RIO as a web page is used to control the scanning parameters. In addition, a fast electrostatic beam blanking trigger has been included in the FPGA and high speed counters (15 MHz) have been implemented to perform dose controlled irradiation and on-line images on the GUI. Analog to Digital converters are used for the beam current measurement and in the near future for secondary electrons imaging. Other functionalities have been integrated in this controller like LED lighting using Pulse Width Modulation and a "NIM Wilkinson ADC" data acquisition.