Here's a quick one liner that will find files by name in the current and all sub-directories and delete them. Tailor it to suit your needs:
find . -name '.DS_Store' | while read pth; do echo "pth=$pth"; rm $pth; done
Hope that helps!
UPDATE Alternate version:
Ran into an excuse to use this today:
find . -name '.DS_Store' -exec rm -f {} \;
The -exec tells the find command to run the following command foreach result it finds. The {} is the placeholder for the found path. The \; bit is the escaped terminator (;) for the command to be executed.
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