Encrypted flash drives

Well, that entirely depends on how exactly the stick is encrypted and whether the encryption format is open and/or if there is API for manipulating encrypted content.

Are you asking if there are encryption options that would allow for that? If so, yes there are. For example, you can use TrueCrypt to format a USB stick as an encrypted volume, mount it as needed and move data back and forth. Furthermore, if you are looking to obscure and hinder the access, you can take TrueCrypt sources and change them to access the volume from your app directly, without mounting it. It all really depends. Your question is just way to general.