Polyimides of Matrimid 5218 and P84 as backbone and different fillers including silica aerosil, zeolite 4A, carbon nanotubes, and carbon molecular sieves were used to synthesize flat mixed matrix membranes (MMMs). Effects of different polymer types and concentrations, different filler types and contents, and fabrication procedure were investigated. Scanning Electron Microscopy (SEM) analysis showed acceptable connections between the two phases and the MMMs performed higher performance compared to the polymeric membranes. Thermal treatment of the MMMs, as a defect repairing technique, was found very effective. Performed pervaporation and gas permeation experiments showed better separation performances of the MMMs with respect to those of the neat polymeric membranes. The results showed up to seven and two times increment in separation factors of MMMs regarding to neat polymeric membranes for pervaporation and gas separation experiments, respectively, while permeation rates nearly remained constant indicating effectiveness of the proper filler incorporation within polymer matrices approach.