decrypting file from eToken - encryption

I am new to cryptography, hence I want to ask about my company's requirements.
We are using eToken with RSA support.
I have developed a code that encrypt file with public key and stored it in another file.
Now I want to pass the encrypted file to eToken, and here is my issue.
How can I access the eToken from a Java applet?
Is it right that I have to pass encrypted file to eToken and it will decrypt file for me?
How can I do this?

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Extend file upload class to use encryption

Is there an easy/straightforward way to extend the file upload class to encrypt files that are being uploaded? Not just encrypting the filename, but rather the data in the file itself.
I'm using mcrypt for db encryption, and would prefer to use the same for file encryption.
Looking through the Upload.php library, I don't see an obvious place where the uploaded file is read which is where I assume I'd shim in the encryption.
Any help/advice would be appreciated.
edit:
What I'm thinking is that somewhere in do_upload() (I'm thinking file_temp) the file gets encrypted before being moved (not copied!) into its final destination. However, I don't see anywhere in Upload.php where the code is working with any of the files' data outside of filename, size, type, etc. Does this approach make sense?

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I decided to forgo modifying the upload class. What I did was after the file was uploaded, open the file, encrypt it, and write it out again.
$f=file_get_contents(BASE_PATH.$fileFullPath) or die ('<script>window.parent.transUpdateFail(\'no gfc'.$fileFullPath.'\');</script>');
$encf=$this->encrypt->encode($f,$this->e_key) or die ('<script>window.parent.transUpdateFail(\'no encrypt\');</script>');
$nf=fopen(BASE_PATH.$fileFullPath,"r+") or die ('<script>window.parent.transUpdateFail(\'no open '.$fileFullPath.'\');</script>');
$fw=fwrite($nf,$encf) or die ('<script>window.parent.transUpdateFail(\'no fwrite\');</script>');
fclose($nf);

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