Nanometer scale morphological order of macroscopically amorphous polyesters, obtained from the melt at moderate cooling rates, was observed in the past. The effect of such order on mechanical properties of a PET/PEN blend, evaluated by AFM nanoindentations, is reported in this study. Results show that nanoindentations conducted at relatively high load, with penetration depths of the order of 100 nm, confirm the information obtained from mechanical tests at micrometer scale, i.e., microhardness. On the other hand, true nanometer scale indentations (<40 nm) are seen to discriminate between the mechanical properties of the nanophases formed during solidification.