Simply add the item into your web-based admin product manager and set "Charge Shipping For This Item?" to "NO" and then set the product weight to 0 (zero).
How do I offer a service-only item for sale on my website with no shipping, etc?
The item will now be excluded from any shipping calculations.
Also, if you will be offering the item as labor (example: installation, support, etc), you will probably want to set "Charge Sales Tax?" to "NO" as well. Typically you would not want to charge state sales tax on service (labor).