The electron-electron correlation in nonsequential double ionization (NSDI) from aligned molecules by linearly polarized 800 nm laser pulses has been investigated with the three-dimensional classical ensemble model. The result shows that for the perpendicular alignment the two electrons involved in NSDI more likely exit the molecule into the opposite hemispheres as compared to the parallel alignment, which agrees well with the experimental result [Phys. Rev. Lett. 95, 203003 (2005)]. This alignment effect is qualitatively explained based on the suppressed potential barriers which are different for parallel molecules and perpendicular molecules. Additionally, the intensity dependence of the alignment effect is also explored.