Copy only certain file types from a folder structure to another

If the tree of directories is more than just ..../f03 you can use this rsync command to copy every fo1 & fo2 and exclude every other directory with the name fo*.

$ rsync -avz --include='fo[12]/' --exclude='fo*/' \
      Main_Dir/ new_Main_Dir/.

When dealing with these types of copy scenarios I always make use of rsync and it's --dry-run & --verbose switches so I can see what it's going to do without actually having to copy the files.

$ rsync -avz --dry-run --verbose --include='fo[12]/' --exclude='fo*/' \
      Main_Dir/ new_Main_Dir/.

Example

Dry run.

$ rsync -avz --dry-run --include='fo[12]/' --exclude='fo*/' \
      Main_Dir/ new_Main_Dir/.
sending incremental file list
./

Subdir1/
Subdir1/fo1/
Subdir1/fo2/
Subdir2/
Subdir2/fo1/
Subdir2/fo2/
Subdir3/
Subdir3/fo1/
Subdir3/fo2/

sent 201 bytes  received 51 bytes  504.00 bytes/sec
total size is 0  speedup is 0.00 (DRY RUN)

If you want to see some of rsync's internal logic as to what is being included/excluded then make use of the --verbose switch.

$ rsync -avz --dry-run --verbose --include='fo[12]/' --exclude='fo*/' \
      Main_Dir/ new_Main_Dir/.

sending incremental file list
[sender] showing directory Subdir1/fo2 because of pattern fo[12]/
[sender] showing directory Subdir1/fo1 because of pattern fo[12]/
[sender] hiding directory Subdir1/fo3 because of pattern fo*/
[sender] showing directory Subdir2/fo2 because of pattern fo[12]/
[sender] showing directory Subdir2/fo1 because of pattern fo[12]/
[sender] hiding directory Subdir2/fo3 because of pattern fo*/
[sender] showing directory Subdir3/fo2 because of pattern fo[12]/
[sender] showing directory Subdir3/fo1 because of pattern fo[12]/
[sender] hiding directory Subdir3/fo3 because of pattern fo*/
delta-transmission disabled for local transfer or --whole-file
./
Subdir1/
Subdir1/fo1/
Subdir1/fo2/
Subdir2/
Subdir2/fo1/
Subdir2/fo2/
Subdir3/
Subdir3/fo1/
Subdir3/fo2/
total: matches=0  hash_hits=0  false_alarms=0 data=0

sent 201 bytes  received 51 bytes  504.00 bytes/sec
total size is 0  speedup is 0.00 (DRY RUN)

If you need to exclude other forms of directories you can add multiple excludes.

Here's the solution on non-embedded Linux and Cygwin:

cp -as SOURCE/ COPY

Note that SOURCE must be an absolute path and have a trailing slash. If you want to give a relative path, you can use

cp -as "$(pwd)/SOURCE/" COPY