The mechanical loading induced flow of glassy polymers is triggered by the nucleation of shear transformation units, and strongly depends on the initial microstructural state of the material. Therefore, investigation of the possible relationship between the microstructural state variables and plastic deformation is required for a better understanding of the macroscopic response of this class of materials during large deformation. In this study, free volume content is considered as a state variable and thermal treatment is selected as a process through which the accelerated and forced evolution of the free volume can be imposed. For two well-known glassy polymers, poly(methyl methacrylate) and polycarbonate, the free volume content alteration upon annealing is monitored via positron annihilation spectroscopy, and the changes of the micro-and macromechanical properties are also obtained by utilizing nanoindentation technique and employing the homogeneous amorphous flow theory. The correlation between the microstructural state variable, that is, free volume, and the micromechanical state variable, that is, shear activation volume, is then investigated. The results reveal opposite direction of alterations of free volume and shear activation volume with annealing temperature. Accordingly, the possibility of the existence of an interrelation between these two state variables is critically discussed.