First this is the Desktop AUDIO section, not the forum section for your question. The "Productivity Software" section would probably have been the most applicable.
In order to "clone" the hard drive, you will need either another internally connected hard drive or an external USB connected hard drive and a program such as Acronis True Image Home (what I use and what most of the techies that I know use) for this. I do regular "full" backups (not incremental backups) of my hard drive, with all partitions to a USB connected hard drive. You can't really do it to a "flash drive".
Dimension E510 with D925 CPU and Vista Home Premium 32 bit
Home Built PC with Q6600 CPU, 8GB RAM, HD4850 Video, HTO Striker 7.1 Audio Card - Windows 7 64 bit Professional
Sonar 8.5.1 ( Producer) DAW Software/Focusrite Saffire Pro 40 Recording Interface and Frontier Tranzport wireless controller.