If your file is hosted by FileMaker Server there's a few options here:
- use the FileMaker PHP API/Custom Web Publishing to hook the online form into your database so that on submit it creates a new record
- if you're using FileMaker Server v13 you can use the new WebDirect feature to do the same using a layout you design
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alternatively you could quite easily parse the email generated by the form. If you have an email plugin, FileMaker could receive the webform emails automatically. All this would work with a normal FM Pro without a server.
Another option is to tap the back-end database the web form is currently using (most likely some form of SQL) using ESS, ODBC, or some form of export.