Duplicate file structure post reinstallation of XP Pro

Reinstalled XP Pro on my Dimension 8400. On installation was asked if I wanted to use the current file structure to which I replied yes and now I have loads of duplicate files.  My original installation was called "My surname" and XP gave the new installation the name "My surname followed by a string of letters and numbers.  Microsoft Updates do not now install because, I assume, it finds previous updates in my old OS installation.  Also, in my old installation I had upgraded IE6 to IE7.  Now on reinstalling my HP PSC 2355 printer/scanner on booting my PC I keep getting msi installer trying to install ImageMaker, but it won't install even when I run my printer install disk.  I understand that there is a conflict between some HP software and IE7, so again my old OS installation is causing problems I think.  How might I safely get rid of my old file structure without compromising my new installation and sort out the other problems I am experiencing please?