I assume that you've opened the PDF with a SetReportFile, and have then applied the model with SetModelFile, and this is where Monarch needs your manual input before the program code can continue, as the PDF Import Options dialog is being displayed.
The only way to avoid this behaviour is to load the PDF and the model simultaneously by saving them together as a project file, and then opening the project file using SetProjectFile instead of SetReportFile and SetModelFile.
Of course this means that your PDF file will need to have the same filename as that which was used to create the project file. If necessary, copy the original PDF (with the named that isn't what Monarch expects) to a new file with the name that Monarch does expect, and then open the project file. There are probably other alternatives to resolving this as well.
I don't do a lot with PDF's but I do have one VBA script that runs automatically. I don't use project files because 99% of the files I work with have a date in the file path so projects won't work.
What I've done is after you create your model, go to "Options" - "PDF Import Options" and in the lower left section of the box uncheck the "Show this dialog automatically" box and you won't get that prompt and your script will run unattended.
Sorry Kruncher for stepping on your post.