rsync is useful for local file copying as well as between machines. This will do what you want:
rsync -avm --include="*.jar" -f 'hide,! */' . /destination_dir
The entire directory structure from . is copied to /destination_dir, but only the .jar files are copied. The -a ensures all permissions and times on files are unchanged. The -m will omit empty directories. -v is for verbose output.
For a dry run add a -n, it will tell you what it would do but not actually copy anything.