Every branch in me that does not bear fruit he takes away, and every branch that does bear fruit he prunes, that it may bear more fruit. (John 15:2)
Gardeners often cut back the early growth on some plants to focus the energies of the plant towards produce more growth. For example, if you prune tomato plants to remove extra shoots then you are likely to get more tomatoes. This is the basis of Jesus’ analogy.
For God to prune Christians may simply refer to God shaping their lives in general to help them towards spiritual growth. However given the analogy is about cutting away young shoots, this may be more specifically about suffering.
The Bible refers to Jesus learning through suffering (Hebrews 5:8) and to believers being disciplined to yield “fruit of righteousness” (Hebrews 12:11). So this seems to be what Jesus has in mind when he talks about pruning.