You are able to delete a payment from TM3 however it is important to note that you can only delete a payment which is unreconciled. If invoices are reconciled against the payment you want to delete then you should unreconcile these otherwise it will greatly affect your finances.
Search for the payment you wish to delete and click 'View.'
The 'Edit Payment' screen will then be displayed. To delete this payment, simply click on 'Delete this payment' at the bottom of the window.
Once you click on 'Delete' a confirmation box will appear and you should click 'Yes' to delete or 'No' to cancel.