The skipper CCD is a special type of charge coupled device in which the readout noise can be reduced to sub-electron levels by averaging independent measurements of the same charge. Thus the charge in the pixels can be determined by counting the exact number of electrons. The total readout time is proportional to the number of measurements of the charge in each pixel. For some applications this time may be too long; however, researchers usually are interested only on certain region within the matrix of pixels. In this paper we present the development of a smart skipper readout technique that allows the user to specify regions of interest of the CCD matrix where an arbitrary (high) number of measurements of the same charge can taken to obtain the desired noise level, and far less measurements are performed in those regions that are less interesting to the researcher, therefore reducing the total readout time.