It sounds like you are already successfully uploading the file.
You have asked a very general question, and there are a huge number of possible answers depending on how you are currently doing it, and what sort of things you are worried about.
I presume you are using the
Apache Commons File Uploads component to upload files right now?
How do you see that as a security challenge?
What are you trying to protect against?
I don't think the
java file upload processes can provide much more than you already have.
I think the easiest solution might be to lock down access to the server, and put the uploaded files in a 'quarantine' area.
How large are the files you are dealing with?