Hybrid manufacturing technology has been advanced to overcome limitations due to traditional fabrication methods. To fabricate a micro/nano-scale structure, various manufacturing technologies such as lithography and etching were attempted. Since these manufacturing processes are limited by their materials, temperature and features, it is necessary to develop a new three-dimensional (3D) printing method. A novel nano-scale 3D printing system was developed consisting of the Nano-Particle Deposition System (NPDS) and the Focused Ion Beam (FIB) to overcome these limitations. By repeating deposition and machining processes, it was possible to fabricate micro/nano-scale 3D structures with various metals and ceramics. Since each process works in different chambers, a transfer process is required. In this research, nanoscale 3D printing system was briefly explained and an alignment algorithm for nano-scale 3D printing system was developed. Implementing the algorithm leads to an accepted error margin of 0.5% by compensating error in rotational, horizontal, and vertical axes.