Look for a common pattern in your files (eg: they are all *xls files). It will be helpful if you can put them all in the same directory (eg: ~/shred).
Code:
mkdir ~/shred
cd dir1/
mv *xls ~/shred
cd ../dir2
mv *xls ~/shred
cd ~/shred
for i in `ls *xls`; do
shred -vzu $i;
done
What we've done is:
1. Created a directory (~/shred)
2. Moved our files to it (mv *xls ~/shred)
3. Changed our current working directory to the shred directory (cd ~/shred)
4. Iterated through the directory listing (for i in `ls *xls`; do)
5. Shredded each file (shred -vzu)
hth