Any 2D array can be represented with a vector, which is the normal input to optimization functions, so all you need to do is write your function to take a vector as input and them convert it to a matrix. A minimalist example:
x = randn(7); % Original matrix
opt = fun(x(:)); % Convert matrix to a vector for function
function opt = fun(x)
x = reshape(x,7,7) % Convert vector to matrix
%... your functio
end
