These templates are usually the ones stored inside the "1033" folder.

You should be able to do something like this:

Sub DelTemplates
Dim sPath as String
Dim sName as String

sPath="C:\Program Files\Microsoft Office\Office\Templates\1033\"

sName = Dir (sPath & "*.dot")

While Len(sName) > 0
   Kill sPath & sName
   sName = Dir()
Wend

End Sub

Alternatively, if you don't want to actually delete the templates, you can
hide them from the "New Document" screen by just applying the "Hidden" flag.  
You can still create documents from Hidden templates using VBA (Document.Add
Template:="Hidden Template.Dot").