after the changes done if i give crtl+s means it again save as two same named parts in my folder
When you save, Creo creates a new file on disk. First one is [part_name].prt.1, next is [part_name].prt.2, next is [part_name].prt.3, etc. When you open a file, Creo only shows the one and opens the latest one.
Do a search here for the purge utility which you can use to clean out the old versions.
Open system window. Type purge and enter.
All the older versions will be removed.
I've attached a program that can purge all files in a designated folder and any subfolders within. It's not the latest version, and I can't point you towards the correct site to download it, only shady ones. The attached version works with Creo 3.
You just change the directory, hit purge, and every Creo file with multiple versions will be trimmed down to only the last version.