We describe the manipulation of the charged state of nanoscale organic "dot" structures using the atomic force microscope, Electric charges were injected into single dots by contact electrification from an atomic force microscope tip to which voltage was applied. On measuring the charge distribution two-dimensionally, it was found that the injected charges were stably confined in the dot structures for an extended period. The number of injected charges could be controlled down to single elementary charge. Further, injected charges could be reextracted from the dots by using a tip with reduced applied voltage. However, complete extraction from highly charged dots was difficult, which suggests that some transfer of charge from dots to adjacent regions may occur.