In this study, the Focused Ion Beam (FIB) instrument has been used for carbon nanotubes integration and nanoegineering studies. Results of thorough investigation (electrical, structural and chemical) of ultra-thin Pt contact lines and pads fabricated by the FIB, along with evaluation of nanomodification of the carbon nanotubes under the Ga+ ion beam and during Pt deposition are presented. The initial stages of FIB-assisted Pt deposition on multi-wall nanotubes are studied by transmission electron microscopy (TEM). The FIB parameters are optimized to provide non-destructive imaging and controllable Pt deposition with minimal damage on the nanotubes. We have demonstrated effective use of FIB-fabricated Pt pads as means of attaching the nanotubes to the substrate for atomic force and ultrasonic force microscopy studies.