Question

1. Take out a pencil out of the pencil case.

2. Take out a pencil from the pencil case.

3. Take out a pencil in the pencil case.
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Are they all grammatical? Does #1 mean #2? Which one is a common expression? Is #3 okay? Does #3 mean that there is only one pencil?

Answer 1

1 -- remove the first "out"
2 -- remove "out"
3 -- Awkward sentence, but it's not incorrect. The prepositions "out of" and "from" are better for this meaning.

All of them seem to mean to take out one pencil from many in the pencil case.