What barcode type are you using? Many can be printed directly from FileMaker simply by installing the needed font, not additional software needed. Some require additional characters used in error checking and such and a calculation field can provide the needed additional characters from a field where you enter the code to be used.
UPC codes on the other hand, have to be registered with the appropriate organization (haven't had to do this myself) in order to ensure that everyone uses a unique code for their universal product codes.
We are wanting to use 2D Data Matricies because the lids on each sample are very small. I don't know if this function is supported in Filemaker.
Thanks for your suggestion however.