Bovine insulin molecular aggregates, a nano-scale bio-entity, has been manipulated using P-NUVO (Programmable nanomanipulation using vibration-mode operation AFM) method. This method uses the amplitude of an AFM cantilever's vibration as real-time feedback information to detect the boundary of the nano-entities under manipulation. This amplitude signal changes as a function of the distance between the probe-tip and a nano-entity due to their inter-molecular force interactions. The AFM tip's manipulating path could also be planned according to the manipulation task. Different configuration of bio-nano-entities, i.e., sphere and rod configurations were manipulated. Due to the difficulties of the sample preparation process, the real-time feedback information did not work as well as for other nano-entities such as carbon nanotubes.