DEP is one of promising techniques for positioning nanomaterials into the desirable location for nanoelectronic applications. In contrast, the lithography technique is commonly used to make ultra-thin conducting wires and narrow gaps but, due to the limit of patterning resolution, it is not feasible to make electrical contacts on ultra-small nanomaterials for a bottom-up device fabrication. Thus, integrating the lithography and dielectrophoresis, a real bottom-up fabrication can be achieved. In this work, the device with the nanogap in between two nanofinger-electrodes is made using electron-beam lithography from top down and the ultra-small nanomaterials, such as colloidal PbSe quantum dots, polyaniline nanofibers, and reduced-graphene-oxide flakes, are placed in the nanogap by DEP from bottom up. The threshold electric field for the DEP placement of PbSe nanocrystals was roughly estimated to be about 8.3 × 104 V/cm under our experimental configuration. After the DEP process, several procedures for reducing contact resistances are attempted and measurements of intrinsic electron transport in versatile nanomaterials are performed. It is experimentally confirmed that electron transport in both PbSe nanocrystal arrays and polyaniline nanofibers agrees well with Prof. Ping Sheng's model of granular metallic conduction. In addition, electron transport in reduced-graphene-oxide flakes follows Mott's 2D variable-range-hopping model. This study illustrates an integration of the electron-beam lithography and the DEP techniques for a precise manipulation of nanomaterials into electronic circuits for characterization of intrinsic properties.