Usually when this argument is presented it uses a diagram like this, to make it easier to visualise:
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Faraday tells you that ##\mathcal{E} = - \frac{d\Phi}{dt}##, where ##\Phi## is the magnetic flux through a surface which is bounded by a closed curve around which the EMF is ##\mathcal{E}##. In this case, you can consider the EMF around a curve running through the rectangle including the moving wire, and the magnetic flux through the two dimensional surface that the curve encloses.
Then you use that, in this case, ##\Phi = \vec{B} \cdot \vec{A} = BA \implies \frac{d\Phi}{dt} = B \frac{dA}{dt} = BLv## to deduce that ##\mathcal{E} = - BLv## (I take that the normal to the surface, ##\hat{n}##, points in the same direction as the magnetic field).
Another way you can derive the same thing is to consider an equilibrium of the magnetic (due to external ##\vec{B}## field) and electric forces (due to charge separation inside the wire) on a charge element inside the wire. You will have$$q\vec{v} \times \vec{B} + q\vec{E} = 0 \implies \vec{E} = -\vec{v} \times \vec{B}$$If ##\vec{v}## and ##\vec{B}## are orthogonal, then the result is ##\vec{E} = -vB \hat{x}##, where we've just oriented our Cartesian axes so that ##\hat{x}## is parallel to the wire. Then$$\mathcal{E} = \int \vec{E} \cdot d\vec{r} = \int_0^L E_x dx = -BLv$$