I had the same problem:

Microsoft includes a command-line utility with Certificate Services called certutil. This utility performs various operations on certificate files, including converting them to and from base64 format.

Note that this command is run on your certificate server, which, in your environment, may be different from your Exchange server. If so, you need to copy the binary .req file to the certificate server, or make it accessible via a shared network folder or removable storage device.

Open a command prompt on the certificate server and navigate to the folder where your binary .req file is, then type the following command:

certutil -encode yourbinaryinputfile yourasciioutputfile

Example:
certutil -encode der.exchange.example.com.req pem.exchange.example.com.req
You can then open the output file in Notepad and confirm that it is in the correct format to upload to your certifying authority.