You can try rsync in place of scp, so that the directory structure is created/preserved on the local machine:
rsync -e ssh -avz user@remote:/modeldir .
If you want to copy just some files, use the proper include and exclude options. The following includes all the directories, includes all the files whose name: start with "file" and exclude the rest
rsync -e ssh -avz --include='*/' --include='file*' --exclude='*' user@remote:/modeldir .