It is my understanding the term non-linear manifold simply refers to the target space of non-linear $\sigma$-models in the literature. To be explicit, consider for example the $O(3)$ $\sigma$-model,
$$S = g^2 \int \partial_\mu n^a \partial^\mu n_a + i \theta \, H(n^a)$$
where $n^a$ is a unit vector field ($n^a n_a=1$) in $2+1$ dimensional space and $H$ is the Hopf invariant. At any time, for finite energy solutions, one has the boundary condition, $n \to (0, 0, 1)$.
In this theory, space-time may be identified with $CP^1$ (or equivalently $\mathbb C \cup\{\infty\}$) and the configuration space consists of maps $S^2 \to S^2$. The manifold is referred to as a non-linear manifold in this context.
More generally, a non-linear $\sigma$-model may be written as,
$$S=\int_\Sigma g_{ab}(\phi) \partial^\mu \phi^a\partial_\mu \phi^b$$
where $\phi^a$ map from $\Sigma$ to some target space $M$. Notice the 'non-linear' part is that the metric tensor is allowed to be a function of the fields themselves, and is contracted with the fields.
Essentially, we can write any non-linear $\sigma$-model in such a way that the collection of fields $\phi^a(x^\mu)$ can be viewed as embedding functions of some manifold $\Sigma$ in $M$.
For example, for the $O(3)$ model, solving the constraints in terms of some parameter (interpreted as a field) and substituting it back into the action will cast it in this form.