Hmm do you want something like a matrix of only the selected terms and everything else zero? If so, then:
julia> Ynew = zeros(5,5)
5×5 Matrix{Float64}:
0.0 0.0 0.0 0.0 0.0
0.0 0.0 0.0 0.0 0.0
0.0 0.0 0.0 0.0 0.0
0.0 0.0 0.0 0.0 0.0
0.0 0.0 0.0 0.0 0.0
julia> Ynew[inds] .= Y[inds];
julia> Ynew
5×5 Matrix{Float64}:
0.0 0.0 0.0 0.0 0.0
16.0 11.0 12.0 0.0 11.0
13.0 20.0 0.0 0.0 0.0
0.0 0.0 0.0 12.0 0.0
15.0 13.0 15.0 0.0 0.0
Otherwise, what Y[inds] does is return a vector of all the values in Y that match your criterion. That is, inds is a vector of indices that match your criterion and then you get a vector out of Y of those corresponding indices. Does this make sense?