No. Pinker indexes the files in the drives and folders that you specify and stores this index in a special Pinker folder on your computer. It does not change any of your files.
Some additional information for the technically minded: you can even remove the special Pinker folder (while Pinker is not running). The next time you start Pinker it will behave as if you had done a fresh installation. On Windows, the special Pinker folder is typically C:\users\<user account>\AppData\Local\Pinker\. On Mac, it is typically ~<user account>/.pinker/.
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