Hill Cipher with unequal matrix
To make the plaintext matrices equal, you could use padding with a null character, such as using "X". For example with "ATTACKS", you would get the following vectors:

$$
\begin{bmatrix}A\\T\\T\end{bmatrix}\ \begin{bmatrix}A\\C\\K\end{bmatrix}\ 
\begin{bmatrix}S\\X\\X\end{bmatrix}\ 
$$