Are you capturing the lines that begin with "Dept:"?
If so, you can define those lines with a detail template, and add the TOTAL line as a footer.
This will cause Monarch to ignore the last total as there aren't any associated detail lines for it.
Otherwise, we'll need to look at another approach.
Dept: 03 Nicola London MD Dr: 3 London MD, Nicola A 1 06/05/2007 99395 39.39
Dept: 03 Nicola London MD Dr: 3 London MD, Nicola A 1 09/11/2007 99212 40.00
Dept: 03 Nicola London MD Dr: 3 London MD, Nicola A 1 12/11/2007 99212 40.00
TOTAL DUE: 119.39
TOTAL DUE: 6,000.17
Edit to show format intended.
Further to Kruncher's suggestion - if you are capturing the detail lines forget the totals and let Monarch calculate them for you in a Summary?