Encrypting Data that is later Backed Up Online

I have to encrypt my files on my work notebook because they are very sensitive, particularly if my computer is stolen. I use an online backup service to back up files daily to an internet service (Mozy). This online service is very fast because it only backs up the files that changed that day. I want to continue to use the offsite service.
Now, if I choose to encrypt the entire disk (as with Apple's program), if I use Mozy, everyday when it does its thing it will want to do a full backup of the entire disk. What I need to do is to find a reliable program that can encrypt all individual data files on my computer. Then, when I do a backup each day, the only files that would have changed would be backed up, not everything else I have already previousy backed up online. I need a solution which automatically encrypts and decrypts as I use the individual files?
I need ideas on what programs to use. I want a good one from a reliable and lasting company, not freeware, because this is sensitive corporate data. Any ideas?

If it were me, I'd get a new hard drive or SSD and put it in an external enclosure. Boot into the recovery partition, format the new drive (not the old one) and install the OS to it. Shut down the Mac, open it up, and swap the drives. You may be able to read your data from the old one externally if you're lucky. If you're very lucky you may be able to use Migration Assistant to move all your stuff to the new drive.
Look at ifixit.com for the exact procedure to get to the drive on your model. If it's a unibody it's pretty simple.
http://www.amazon.com/Sabrent-2-5-Inch-Aluminum-Enclosure-EC-TB4P/dp/B005EIGUD4/ ref=sr_1_3?ie=UTF8&qid=1392154588&sr=8-3&keywords=2.5+enclosure

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