Monarch knows a lot about the data and format it is exporting. But it does not know how to ID an Index Field. This must be done within the Database itself.
Once the data has been exported to Access, open the MDB file and go to Design View. Choose the Field you would like to use as an Index and adjust the Index Properties in the General Tab to reflect your Index requirements.
Save the changes.
DWCH Tech Support
Assuming that you're working with the same fields every time you rebuild indexes, would it be a reasonable solution for you to create an update query in your database that creates indexes for you via SQL code (CREATE INDEX ...)? This would take most of the tedious manual part out of the equation.
If you're exporting from Monarch to a new mdb file with only one table, you could write an update query in your main database to import the freshly exported table into the main db and then build the indexes you need on that new table.
Just an idea. Is something like this worth pursuing for you?