AxCrypt can encrypt most of the file types. Also some file types AxCrypt will not encrypt due to security reasons.
You can encrypted the pdf file with AxCrypt app.
AxCrypt will not encrypt any system, hidden files and operating system installed drives/folder. So please avoid securing that kind of folders.
Because AxCrypt encrypted files will have a special file extension .axx and those will be opened only with the AxCrypt app.
If the above does not help,please provide more information about the issue and write a mail to firstname.lastname@example.org . you can send a screenshot showing where the problem is, it often helps us understand.