protecting two different folders with forms authentication

The authorization? settings in web.config affect all files and subfoldersby default wiht the same settings. If you want to change the settings forta specific file or directory you can use the location element:
configuration
system.web
system.web
location path="SomeSubDir"
system.web
authorization
allow roles="Admin"
deny users="*"
authorization
system.web
location
configuration
use open and close angular brackets.

Happy Programming