You can use the Suppress Invoice feature to exclude or suppress certain invoices while performing an invoice run. In some situations like invoices with zero amount or with a small value (low amount) you might not want to generate an invoice for sending it to the customer. Such invoices can be removed from the Invoice Runs, so that they are not sent out. 

For example, you are an executive in the Billing department of a software company. You want to perform an invoice run but want to suppress invoices for accounts that have a due amount less than $0. To achieve this configuration, you can select a modifier 'Less than or equal to' from the picklist and specify the amount (Zero in this case).

The amount you specify must include all applicable taxes.

If you cannot see 'Equal to' modifier in the Suppress Invoices picklist, please refer Custom Settings to add it to the list.