An audio editor. A free one which is just as good as but a little slower than some commercial ones is Audacity (click on link. But be sure to also download the manual & extras which are separate downloads.

Doing it manually using an audio editor is safe. Be sure to save all your edits in wav or aiff format. Then when you are happy convert to mp3. Or else if for burning, then burn directly from wav/aiff format. mp3 is a compressed format that throws away audio information to help save in size, thus every time you save into that format the quality & frequencies & tone become thinner and thinner. So always save your work in a lossless format like wav or aiff until you are finished with what you wish to do. And yes, best to burn from wav or aiff than mp3.

Oh .. and always make back up copies after each thing you do so you don't need to repeat everything in case you make a mistake. After completion when you are happy with it, the backup copies can be deleted.