As you need to remove a large amount, I assume that you want to use some form of script.
IIS 6.0 using IISvdir.vbs ( @MSDN article ):
At the command prompt, use the cd command to go to the directory where the Iisvdir.vbs script is installed. By default, systemroot / system32 / iisvdir.vbs is used for this file.
At the command prompt, type:
cscript iisvdir.vbs /delete "Sample Web Site" VirtualDirectoryName.
- . - , -, .
IIS 7, AppCmd.exe ( @TechNet):
, :
appcmd delete vdir /vdir.name: string
vdir.namestring - .
, contoso, :
appcmd delete vdir /vdir.name: contoso / photos
marketing contoso, :
appcmd delete vdir /vdir.name: contoso / marketing / photos