Delay Parts Of A Macro From Running

I have created a macro that goes to a report application. The report application runs a script that extracts certain parts of various reports (the script asks for user input to pull the various reports) and exports the data to a spreadsheet. The script gets one report, writes the data to a spreadsheet, gets the next report, appends the data to the spreadsheet, etc. The macro then moves and formats the data in a customized way to be put to second spreadsheet. My problem is that the macro tries to format the data before the script has completed - how can I stop the macro from running until the script has finished? The script varies in run time - anywhere from 1 to 5 minutes.