I have two images I would like to align. Autoalign is not possible because the images display the same place in different weather conditions. Is it possible that I select few control points (building corners, streetlamps, street etc) that should be aligned and the rest of the image would align via interpolation?
Yes. You can do this quite easily in Hugin, a popular open source Guide tool for panorama creation and other image alignment tasks. You can read about the details in the corresponding page of the manual, but it really just comes down to going to the control points tab and adding them by clicking. (There's no special trick to it; it's part of the program's basic functionality.) As the docs suggest, you should have at least three points per image for basic corrections, and more for more complicated ones.
You also might try automatic point selection; depending on the images, it may work better than you expect.