In general this cannot be done. This is because of the existence of Bernstein sets. $B \subseteq \mathbb{R}$ is a Bernstein set if both $B$ and $\mathbb R \setminus B$ have nonempty intersection with every uncountable closed set. In particular such sets do not contain any uncountable closed subset.
Of course, such sets are not very pleasant: they do not have the Baire property, and they are not Lebesgue measurable. For Borel subsets of $\mathbb R$ we have a positive result in the form of the perfect set property: every Borel subset of $\mathbb R$ is either countable, or contains a perfect subset.
For the specific case of the irrational numbers, there are several constructions given in this previous question: