Well I found a way, maybe not the best one but it works so far for what I needed to do, so, if it can help anyone...
for i = 1:1:numel(app.tree.CheckedNodes)
app.sDATA(:,i) = app.DATA{:,(app.tree.CheckedNodes(i).Text)};
end
where DATA is a table where the VariableNames are identical to the tree nodes text labels.