There are several programming libraries out there which give you easy-to-use PDF data extraction tools. For C# I know about Bytescout and Leadtools. I'm however not sure if they offer checkbox detection.
If you don't want to develop the data extraction yourself, you can check out Docparser. It's an app which allows you to extract data from PDF files without coding. Once set up, you can import documents and obtain the parsed data with through a HTTP API.