Probable answer by guessing what you are doing: If all those unwanted pictures are also displayed in the galery, and you use some "media-importing-software" (as opposed to just copying files in explorer yourself):
This importing software is probably contacting your Android device's media server for "media of the type image", so it gets all images returned the media service knows about. No big help up to this, but: You can tell the media service to exclude directories from its library by placing an empty file named
.nomedia there (the leading dot is essential in the file name!). As soon as the media scanner finds that file, the entire directory it resides in (including all subdirectories) is skipped. If there are any pictures, videos or sound files, they won't show up in the galery (but you still can access them via a file browser if you want), and the media service will not even know they exist. So the next time it is asked for "all media of type image", those files won't be mentioned.