I downloaded carbon copy. transferred entire internal hd  to new replacement HD  thru USB.  computer booted from replacement hrdrive. then installed replacement hard rive into iMac. when rebooting imac did not recognized new replacement hd.

  i downloaded carbon copy. transferred entire internal hd  to new replacement HD  thru USB adapter kit.  computer booted from replacement hrdrive. then i erased the internal hardrive and reloaded the operating system.( i needed to find out if the hard drive was bad or virus/worm was the cause). then installed replacement hard drive into iMac. when rebooting, imac did not recognized new replacement hd. i also upgraded memory at the same time.  ok what did i do wrong. do i have to remove the new replacement hardrive to extract the data.

It should not matter. CCC will "clone" the recovery partition as well, but not knowing exactly what operation you had CCC perform it is difficult to know what may have gone wrong - it has many customizable options and you have to choose the correct one.
I have performed the same transplant as you described and didn't have a problem, but if your Mac is not recognizing the internal HD you really have no choice other than to reinitialize it as suggested. After that, install OS X, upgrade to Mountain Lion if required, and migrate your old account(s) from your backup.
my backups have backups.
I assume you didn't mean that literally. Have redundant backups - don't "back up your backups".

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