Use a pair of clean pair of scissors or garden clippers to prune any unhealthy roots when repotting a phalaenopsis orchid. Unhealthy roots are brown, soft and mushy.
Prune off the top part of the stem after it has finished its blooming cycle and no more buds are evident. Do this only for mature phalaenopsis that have foliage at least 12 inches tall. Use a sharp, clean knife or clippers to cut the stem. Prune it down about 1/4 inch above a node that is about halfway down the stem, and then seal the wound with candle wax or cinnamon powder. This kind of pruning will encourage the plant to grow a new section of stem, which may bloom again in three to four months.
Prune away any diseased leaves, such blackened leaves caused by a fungal or bacterial diseases. Also, prune off leaves that are blackened due to hard water or overfertilizing. Use a sharp, sterile knife or blade to cut off the leaves to a healthy area.