Proofing Without Codes

I've been trying to export a pdf proof copy from twine. But it always shows the codes too:

<<set $x to 0>>

or

[[LinkText|Passage]]

Is there a way that it would just print the text in the passages and not the accompanying codes too?
(I'm following the suggestion on importing published story from offline version of twine to the web version to export to pdf.)

Using:
Twine 2 2.1.0(Downloadable)
SugarCube 2.16.0(Offline)
Mac OS El Capitan