The question makes little sense. If the disk has file system on it (it does not have to), you simply need to copy the files. In this respect, this is no different from any file copy.
If you need to copy some data on a lower level than the file system, you should explain what you want to copy and how you want to map it on your files. One such piece of data could be a boot record. If you copy it, you would need a mechanism for using it. For example, you could make an ISO 9660 image of the disk (http://en.wikipedia.org/wiki/ISO_9660
]), but not all disks meet this standard. Many utilities do that, but this is not what you are asking about.
And you should understand that if your "brick wall" is copy protection, making a copy could be considered as a crime, depending on the product license you have accepted, directly or indirectly, and legislation.