I would guess that you're supposed to use "homogeneous coordinates", and that the "3D" matrix you're supposed to compute is the matrix of a projective transformation. When we use homogeneous coordinates, a coordinate vector for a point in a plane has three components rather than two. This may seem unintuitive or unappealing, but there are advantages to homogeneous coordinates: 1) "points at infinity" can be assigned coordinates as easily as ordinary points ; 2) every projective transformation is given by multiplication by a $3 \times 3$ matrix. (There are other advantages too; mathematicians have discovered that homogeneous coordinates are a natural and elegant way to assign coordinates to points in a projective plane.)
Suppose we have a projective transformation that is represented by a matrix $H \in \mathbb R^{3 \times 3}$, so that point with coordinate vector $x$ maps to a point with coordinate vector $Hx$. If we have four points $x_1,\ldots,x_4$ in "general position" and we know these four points map to $y_1,\ldots, y_4$, then we can use this information to compute $H$.
We cannot simply say that $y_i = H x_i \, \,$, because one quirky thing about homogeneous coordinates is that if $y$ is a coordinate vector for a point in a projective plane, then any nonzero scalar multiple of $y$ is also a coordinate vector for the same point. This might seem weird but it's something we must get used to.
The most we can say is that $y_i$ is a (nonzero) scalar multiple of $H x_i$. An equivalent way to say the same thing is
\begin{equation}
y_i \times H x_i = 0
\end{equation}
where $\times$ denotes the cross product.
Notice that this equation is linear in the components of $H$ ! For each $i$, we have three linear equations for the components of $H$. However, it turns out that one of those three equations is redundant, so each $i$ really only gives us two equations. All together, we have eight linear equations.
$H$ is found by finding a nonzero solution of this system of eight equations. Note that this only determines $H$ up to a scalar multiple. However, that's to be expected, because in homogeneous coordinates, any nonzero scalar multiple of $H$ represents the same projective transformation as $H$.