Nano assembly and manipulation technologies are the basis for nano-electro-mechanical systems(NEMS). Atomic force mieroscope(AFM) is widely used to manipulate nanotubes to assemble NEMS. Manipulating nanotubes with AFM is a challenging and difficult task. One of the major reasons is the deficiency of visual information during the manipulation process. To address these difficulties, this research aims to put forward novel virtual tools and assembly strategies to improve the efficiency, accuracy and ease of the assembly process of NEMS. This paper begins by the discussion of the principles and implementation of a virtual nano-assembly simulator, which serves as a benchmark to test the proposed NEMS assembly techniques and virtual tools. Then, a general framework of nanotube-based NEMS assembly is proposed. Several nano-assembly strategies and virtual tools, such as automated path planning for NEMS assembly, a four-step scheme of nanotube manipulation, virtual fixtures for assembly finalization and safe manipulation, are introduced. These virtual tools and methods are experimented for justification. An assembly task of moderate complexity was performed in our virtual nano-assembly simulator with and without the help of the proposed toolkit. Experimental results suggest that the proposed methods tend to greatly enhance the efficiency and accuracy of nanotube-based NEMS assembly. In general, the proposed virtual reality toolkit not only ensures the safety, but also enhances the accuracy and efficiency of the assembly of nanotube-based NEMS.