You can do the following:

1) Hide the text you do not want to count: Open each document, highlight the text you do not want to count, right-click on it and choose Font. 
In the opened window select the checkbox "Hidden" in the Effects field. The edited text will be underlined by a dotted line. Save the files.

2) Open Anycount, add the files, in "Settings" switch to the "DOC, RTF, ..." tab, and disable the "hidden text" option.

The program will then count everything except the hidden text.