You can decrypt the wallet data. That way if someone access to your machine can't use it.
I guess you mean to
encrypt the wallet?
Hide the encryption key somewhere else and manually enter it whenever you run the wallet.
You would have to 'hide' the
decryption key (either the same as the encryption key [
symmetric encryption] or called private key [
asymmetric encryption]).
Note that this is effictively not an option since the wallet has to run all the time on the server (depending on the application).
If automated transactions are made, the wallet has to be accessable to the node/software.