Can’t Run AutoSetup.exe

is there a file that runs autosetup when you first install a program. Does Win Xp Home Eddition run Win 98 program. if so. When i insert a cd of a program i run the setup and get an error

16 bit Windows Subsystem

C:\Windows\SYSTEM32\AUTOEXEC.NT The system file is not suitable for running MS-Dos and Microsoft Windows Application. Choose ‘Close’ to terminate the application.

I once had a trojan horse and i remove it using AVG 7.0. How do i get that file back or can i.