You can’t depend on computer programs to properly check your work—not for copy editing or proofreading. Proofreading is typically done on page proofs, once a document has been copy edited and typeset, or in a pdf.
I do a line-by-line read-through and ensure that corrections were made for typos, grammar, spelling, punctuation, inconsistency, and other errors, as well as check for typesetting issues.
By this stage, the number of necessary changes should be quite low. I do not recommend a proofread if your document has not first been completed and copy edited.
§ The fee for proofreading is $60/hour and the average rate of speed is 10–12 pages an hour. Please visit the FAQ page for more information on the process and on how fees and payment work.