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There are three primary techniques I use when trimming stems:

1. Uproot the whole stem plant, and cut off the bottom half or so. Manually pluck the bottom few leaves on the top stem, and plant it back into the substrate with tweezers. I usually use this method for larger stems, especially if the bottom portion is starting to look unhealthy or grow algae, and I want to get rid of it.

2. Leave the stem planted, and prune off the tops. I use this method when I want to encourage branching. Many plants will grow several branching stems if you cut off the top, and you can use this technique to create a "bush" of several stems from a single rooted stem.

3. A combination of 1 and 2 above. Cut off the top half or so of a stem while leaving the bottom half rooted.

Hope this helps. If you do a search for "trimming" or "pruning" you should find several more threads on this subject.

You can also remove the roots growing out of the stem if they appear unsightly during pruning. Or you can leave them. It's up to you. It generally doesn't seem to significantly affect the health of the stem either way.
 

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I only discard the bottom part if its looking ratty. If the plant is healthy and not rotting anywhere, I just cut off the tops into the shape/height I want it to be.
As for the side shoots, if you let those grow out, it will give your plant a bushier look once its grown in. On the other hand, you could always trim it off and replant it as a separate stem, if its long enough.
Also, just know that trimming stems frequently can be a good thing, as it promotes new growth and helps train it to grow how you would like.
 
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