At present 3D PDF files output by MicroStation V8i (also by AECOsim Building Designer and PowerDraft) are not able include the 3D PDF section cutting functions by default. This tool only appears when the files are opened in Acrobat Pro. In Acrobat Reader all the 3D viewing tools except the section cutter are available.
Acrobat Pro adds the section tool to the end of the toolbox:
To get around this open 3D PDF files created by MicroStation with Acrobat Pro, where this capability can be added.
In Acrobat Pro go to the > File menu > Save As > Reader Extended PDF > Enable Additional Features...
Note the restrictions stated below, however, these are unlikely to be a problem for files that are being sent outside your organisation.
Save the file, with a different name, and open in Reader, the section tools will be available. If a page from a 3D PDF where Extend Features has been applied is inserted into another PDF, that PDF will also need to have Extend Features applied, the setting is stored in the PDF file, not in the page. Always test that the tool is visible in Adobe Reader before sending to a third party!
This example is an AECOsim Building Designer file printed to 3D PDF from PowerDraft: