Under some general assumptions, we construct the scaling limit of open clusters and their associated counting measures in a class of two dimensional percolation models. Our results apply, in particular, to critical Bernoulli site percolation on the triangular lattice and to the critical FK-Ising model on the square lattice. Fundamental properties of the scaling limit, such as conformal covariance, are explored. As an application to Bernoulli percolation, we obtain the scaling limit of the largest cluster in a bounded domain. We also apply our results to the critical, two-dimensional Ising model, obtaining the existence and uniqueness of the scaling limit of the magnetization field, as well as a geometric representation for the continuum magnetization field which can be seen as a continuum analog of the FK representation.