This is a likely reference back to both "He takes away" and "prune" from v2. So, both verses in context:
John 15:2-3 (NASB emphasis added)
2 Every branch in Me that does not bear fruit, He takes away; and every branch that bears fruit, He prunes it so that it may bear more fruit. 3 You are already clean because of the word which I have spoken to you.
Prunes & Clean
...We could be looking at a translation inconsistency with prune and clean:
If we translated both as "clean", we would get this...
2 Every branch in Me that does not bear fruit, He takes away; and every branch that bears fruit, He cleans it so that it may bear more fruit. 3 You are already clean because of the word which I have spoken to you.
...or...
2 Every branch in Me that does not bear fruit, He takes away; and every branch that bears fruit, He prunes it so that it may bear more fruit. 3 You are already pruned because of the word which I have spoken to you.
...while different to us in English, to the disciples in Greek, both English translations would have both sounded much the same and carried almost the same meaning.
Takes & Clean
If clean (v3) points to prune (v2), then the next question is whether takes (v2) implies punishment. But, that is not addressed until v6...
John 15:6 (NASB)
If anyone does not abide in Me, he is thrown away as a branch and dries up; and they gather them, and cast them into the fire and they are burned.
..."branches" not abiding in the vine are not vine branches at all! They are invasive weeds, which Jesus talks about elsewhere in the parable of weeds (Mt 13:24-43).
"Branches not abiding in the vine [because they are weeds]" could actually explain the debated meaning of the wedding guest who arrived without wedding clothes and was thus cast out (Mt 22:11-13). What on earth is a non-grape-vine branch doing on top of a real grape vine!? Probably the same thing a so-called "wedding guest" is doing at a wedding without the free clothes provided by the wedding: burglary or such mischief.
Clean: Taken & Pruned
This gives us three types of branches:
- Vine branches not bearing fruit: taken (v2, for health)
- Vine branches bearing fruit: pruned (v2, for more growth)
- Non-vine branches: gathered and burned (v6, for burning)
1 & 2 from v2 become clean in v3.
Number 3 is not a reference to number 1, as we could think reading in English. So, "burning" of v6 is not "clean" of v3 contrasting in v2. No, "clean" in v3 is discussing something good about v2, which has no burning.
So, in all likelihood, v3 "you are already clean" probably means the disciples had already gone through any stages of "take" or "prune" from v2.
From the Believer's Bible Commentary1
John 15:2 ...Exactly what the Lord does to the unfruitful branch depends on how the Greek verb airo is translated. It can mean “takes away” as in the King James tradition (also translated that way in John 1:29). Then it would refer to the discipline of physical death (1 Cor. 11:30). However, the same word may mean “lifts up” (as in John 8:59). Then it would be the positive ministry of encouraging the fruitless branch by making it easier to get light and air, and hopefully, to bear fruit.
...Even such vines need to be pruned or cleansed. Just as a real vine must be cleaned from insects, mildew, and fungus, so a Christian must be cleansed from worldly things that cling to him.
John 15:3 ...Just as the Savior had been talking to them, His Word had had a purifying effect on their lives. Thus, this verse may refer to justification and sanctification.
Since "takes" (airó/αἴρω, Strong's 142) can mean have either a positive or destructive meaning, v3 clarifies that "takes" carries the positive "for cleansing purposes" variety of meaning.
That's why we have "clean" (katharos/καθαρός, Strong's 2513) in v3.
This is another commentary giving teaching this as encouragement and good thing...
From BibleRef.com:
Jesus inserts this comment to clarify the "dead branches" reference: it is not to Christians somehow losing salvation or falling into damnation. Jesus is explicitly reassuring the disciples that they are not among the dead branches.
1. MacDonald, W. (1995). Believer’s Bible Commentary: Old and New Testaments (A. Farstad, Ed.; p. 1549). Thomas Nelson.