MY system folder, including hidden folders are littered with duplicate folders and files with the suffix (from old Mac) How do I remove them

I have a Macbook Pro running Leopard 10.5.8. I had a problem with my my operating system (my fault, I moved a file I shoudnt have) couldnt boot up but was able to boot up from a backup. I managed to repair my original system except now all the system folders, including hidden folders are littered with duplicate folders and files with the suffix (from old Mac).  For the most part the dupes are an exact copy, but not always.  I want to remove them to free up space and cant imagine duplicate folders in the /system/library are not hindering my computer. But I dont know where to start and am afraid of doing irreparable damage. Any ideas

pacull,
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