Click Run to activate the Run Options window, check the Export Format Custom box, click Edit, select the existing format and click Modify (or click new, select format template, click OK) and the Export Format Editor window will be open. In the Spot Properties section, from the Spot Layout pull down menu, select Each Spot As Plate and save the format. Now the exported data will have each spot presented as a 96- (384-) well plate.

The Export Format Editor offers a lot of choices for general file properties, layout properties and header/footer properties. If you have stored a data file in default format, by clicking Select Sample Data and then selecting the default data file, you can view how the custom export data file format will change when selecting the different formatting choices.