Compatibility Mode

I attempted to install windows NT 4.0 on to my windows 98 and in the process I made a mistake, now I am getting a message when I go to my Device Manager(Performance tab) “Drive A,B,C is using an MS-DOS compatibily mode file system”. It also tells methat this mode is slowing down the performance of my computer, also my Device Manager is not reading my CD-ROM, I also have exclamation points on my floppy disk, and hard drive. Can any one help me?