If you choose to copy the files you are converting, instead of converting or filtering them in place, which is a lot safer, the new files created will be structured like this.
Suppose you are processing d:\texts\2007\literature and copying to c:\temp
and suppose d:\texts\2007\literature contains this sort of thing:
d:\texts\2007\literature\shakespeare\hamlet.pdf
d:\texts\2007\literature\shakespeare\macbeth.pdf
...
d:\texts\2007\literature\shakespeare\poetry\sonnet1.pdf
d:\texts\2007\literature\shakespeare\poetry\sonnet2.pdf
...
d:\texts\2007\literature\french\victor hugo\miserables.pdf
d:\texts\2007\literature\french\poetry\baudelaire\le chat.pdf
...
you will get
c:\temp\shakespeare\hamlet.txt
c:\temp\shakespeare\macbeth.txt
...
c:\temp\shakespeare\poetry\sonnet1.txt
c:\temp\shakespeare\poetry\sonnet2.txt
...
c:\temp\french\victor hugo\miserables.txt
c:\temp\french\poetry\baudelaire\le chat.txt
...
In other words, for each file successfully converted or filtered, any same directory structure beyond the starting point (d:\texts\2007\literature in the example above) will get appended to the destination.