Quantum dot single electron transistor (QD SET) is fabricated using e-beam nanolithography (EBL) and is continued with the combination process of pattern dependent oxidation (PADOX) and high density plasma etching. EBL was used to pattern the whole masks of SET fabrication which consist of mask for doped area separator and the rest are for the formation of; source-quantum dot-drain, poly-Si gate, point contact and metal pad respectively. All of these masks were designed using offline GDSII Editor Software and later been exposed by EBL integrated using the scanning electron microscopy (SEM). ln this paper, the whole designs of SET masks which are successively patterned are demonstrated and their nanostructures characterizations using SEM and atomic force microscopy (AFM) are reported. We found that the shape and dimension biases of schematics and SEM images of masks were caused by proximity effect. Therefore, while designing the SET masks, proximity effect, used resist and EBL equipment resolutions were considered.