If I had 5 apples and now out of them I have only 3.
What's the natural way to say it, while emphasizing that remains only three.
1) I have (got) 3 apples left now.
2) Remains me only 3 apples now.
Number 1 is natural and common.
Number 2 is incorrect for a number of reasons.
First, remain is an intransitive verb, so it can't be used with a direct object; it would have to be "remain to me."
Second, that sentence has a verb-object-subject structure, which we rarely see in English (actually, I can't think of an example that's not non-standard or out of date, e.g. "Knew it all along, I did" - which might actually be an elided subject, and then an emphatic repetition). So we would need to restructure the sentence: "Three oranges remain to me."
Third, we don't typically use to or to me with remain, we're more likely to say something like, "Only three oranges remain in my possession."
Fourth, while "only three oranges remain in my possession" is grammatical, and idiomatic, it sounds very formal and precise and thus, we might say something like this in a court room ("Of the five documents obtained by the defendant, only three remain in his possession"), but probably wouldn't say something like this about oranges.
Only 3 apples remain (to me).
or one of the various other conjugations of the verb:
Only 3 apples are remaining.
Only 3 applies have remained.
Or use the existential "there"
There remain only 3 apples.
You can also use "left", although this is the past participle that functions as an adjective:
Only 3 apples are left.
"Remain" doesn't take an indirect object so you would not say "remain me". Instead use the preposition "to".
There remains to Heracles only one of the golden apples he stole from the Garden of the Hesperides.
(Edit) Your first example is fine. Again, it uses the past participle "left" as an adjective, which is natural.
I have now 3 apples left.
The interrogatives of these would be.
Do only three apples remain?
Are only three apples remaining?
Have only three apples remained?
Does there remain only three apples?
Are there only three apples left?