@ Heather, Thanks for your reply. I do use the 'Advanced' options to deselect any unwanted feature classes. The problem occurs when if the feature classes I deselect were in a feature dataset, I get an empty dataset (there is no way to deselect the dataset). Also if there were no features within the Area of Interest graphic, but I leave the feature class selected as I'm unsure of this, I get the empty feature dataset.
I agree this is the default behaviour, probably due to the tool being related to 'distributed' databases, users may create new features to upload and therefore need all the feature classes they've extracted. So the problem is more related to how I'm using the tool, not the tool itself.:) (I don't intend to upload the data I've extracted)
@ JSkinn3, Thanks for the script! I'll give it a try tomorrow and let you know how I go. I'm a noob at scripting/python so it could be interesting. Doing the training soon, hence the preference for a tool, but if one doesn't exist, it doesn't exist.
Many thanks!
-Mick