Lee: you need to make sure you're using proper primes, not just straight quotes (which is what Ctrl-' gives you), as David and Jongware explained above.
If you're on a Mac, you can easily find the actual prime and double prime symbols using the system Character Viewer (Character Pallette in pre-Snow Leopard versions) from the top menubar next to the clock (if it's not there you may need to turn it on in System Preferences > Language and Text > Input Sources). The prime and related symbols are listed in 'Punctuation', or in Snow Leopard you can actually type the word 'prime' into the search box at the bottom and it will find it for you, and then you can click on it to insert at the cursor.
From the Character Viewer you can also see which fonts contain these characters; if you're using them a lot you might want to make sure you're using a font that includes them, or at least (if you don't have control over the font) one that's a better match for your text than Symbol (an ugly font if ever there was one).
Once you have chosen your font, you can do a GREP search to find and replace quotes with primes as described above (you can insert the prime character from the Character Viewer into the Replace box). If you aren't using a text font that includes the prime character, you can then set up a GREP style in your paragraph style to put the primes and double primes into a character style that has the appropriate font.