Go through the song and mark where each section begins and ends. Your song could have any or all of the following sections: intro, verses, chorus, bridge, outro. Some audio editing programs allow you to make markers on a file; otherwise, write out the sections on a piece of paper for reference.
Analyze the chords of the song. Notice where certain harmonic progressions begin and end. To create a smooth edit, avoid shortening or altering these harmonic "sentences." Instead, delete them completely or leave them intact to preserve the flow of the song.
Review the verses of the song. You may be able to cut one or two of them out without losing the meaning of the song. If so, use an audio editing program to cut from the beginning to the end of the verse. Do not cut off any parts of the chorus or the next verse.
Count the choruses. Many songs contain multiple repetitions of a chorus, especially toward the end of the song. Because the chorus always contains the same words, you can delete one or two of these repetitions to make the song shorter.
Delete sections of a lengthy intro. Often, these sections are harmonically simple, repeating musical material that happens in the song. Other times, they are not harmonically relevant to the rest of the song. Delete these sections and begin with the first verse or just leave the last few measures of the introduction.