After doing semantic differential experiment with two different group of people, there is need to do Factor Analysis, and after that to compare group's coordinates in factor space. I did factor analysis separately for two groups, and unfortunately the result is their factor structure are little (or not little) different. What than should I do for compare? Need I to "merge" two groups at one file and make Factor Analysis? Or it would be wrong? I use SPSS.
Rotations in factor analysis are arbitrary. You cannot simply look at the loadings for two groups and determine that they are similar or different, because even identical factor structures may come somewhat rotated relative each other in space (even if you didn't rotate your factor solutions at the analyses). This link will teach you how to compare factor loadings. Using procrustean rotation and congruence coefficient is a nice way to go.
But before you start comparing factor loadings: do you have a good reason why you did factor analysis for each group separately?