The novel instrumentation of nanomanipulation coupled to nanospray mass spectrometry and its applications are presented. The nanomanipulator has the resolution of 10nm step sizes allowing for specific fine movement used to probe and characterize objects of interest. Nanospray mass spectrometry only needs a minimum sample volume of 300nl and a minimum sample size of 300attograms to analyze an analyte making it the ideal instrument to couple to nanomanipulation. The nanomanipulator is mounted to an inverted microscope and consists of 4 nano-positioners; these nano-positioners hold end-effectors and other tools used for manipulation. This original coupling has been used to enhance the current abilities of cellular probing and trace fiber analysis. Experiments have been performed to demonstrate the functionality of this instrument and its capabilities. Histidine and caffeine have been sampled directly from single fibers and analyzed. Lipid bodies from cotton seeds have been sampled indirectly and analyzed. The few applications demonstrated are only the beginning of nanomanipulation coupled to nanospray mass spectrometry and the possible applications are numerous especially with the ability to design and fabricate new end-effectors with unique abilities. Future study will be done to further the applications in direct cellular probing including toxicology studies and organelle analysis of single cells. Further studies will be directed in forensic applications of this instrument including gunshot residue sampled from fibers.