I'd probably recommend using something like rsync for this due to its include and exclude flags, e.g:-

rsync -rav -e ssh --include '*/' --include='*.class' --exclude='*' \
server:/usr/some/unknown/number/of/sub/folders/ \ 
/usr/project/backup/some/unknown/number/of/sub/folders/

Some other useful flags:

  • -r for recursive
  • -a for archive (mostly all files)
  • -v for verbose output
  • -e to specify ssh instead of the default (which should be ssh, actually)