converting xml files in multiple directories to multip

I am currently using Saxon 6.4.3 on Windows 2000 to to transform multiple XML
files in multiple directories. As far as I know saxon can only handle a single
xml file or a single directory as input, but not a whole structure of
directories (including subdirectories). So in a batch file I always have to
call Saxon once for each directory I want to handle. As this is quite time
consuming I would like to use an XSLT processor that needs only one single
directory as input and processes all subdirectories containing the XML files i
want to transform. The output should be done the same way.
Is Saxon capable of doing this? If not, is there any other XSLT processor
available that fulfils my requirement?

regards
Mario Michlits