As a very important material processing technology, plasma processing is able to modify sample surface through etching, deposition, activation, functionalization, polymerization, etc. However, the general plasma processing reacts on a large area of sample surface. Hence a mask is needed for selectively treating the sample surface. In this paper, a plasma integrated atomic force microscopic (AFM) nano manufacturing workcell has been developed, which consists of a micro plasma source and an integrated AFM nanomanipulation system. The miniature microwave plasma discharge applicator is able to create a miniature plasma stream with a diameter ranges from 2 millimeters down to micrometers. Hence the micro plasma will be able to locally treat a sample surface and has the potential to eliminate the requirement of masks. With the integrated AFM system, the sample surface is able to be inspected and further modified at nanoscale in the same chamber after machined by the micro plasma. The system design and implementation are presented in the paper. Experiments have been carried out to demonstrate the effectiveness of the system by locally etching a silicon substrate surface using the micro plasma source.