I am not sure what you need to do and I am not sure I understand what Suthish is saying.
If I understand you then what you can do is to have a list of directories that you are currently processing and then when FileSystemWatcher says a directory has changed then if that directory is in the list then ignore it. Or more precisely, whenever you change something, put it in a queue and then when FileSystemWatcher says it is being changed, remove it from the queue and don't do anything more for that change notification. Assuming that there can be only one file at a time that is relevant, then you only need to do this for one file at a time.
Thinking is a feeling; pleasant for some and unpleasant for others.