Yes, when scheduling your report you can exclude by order status (e.g. you may wish to exclude cancelled orders) or by customer ID (e.g. you may wish to exclude any orders placed by your internal staff). You can of course just remove any order rows you don't want to include in your report from your CSV file before you upload it too.
Any orders with an order value of 0 or less will automatically be excluded from the import process. In addition, any months with zero orders and revenue will be excluded from charts and tables in your report.