How to verify the content of a branch within a Tree?

ROOT
2

You probably want

for (int i = 0; i < 625; ++i) {
    ZRX00 = ZTR[ i ][ 25 ];
    ZRX00 = ZTE[ i ][ 25 ]; 
    ZernikeTree->Fill();
}

First you set the values, then you fill an entry.

See this answer for various methods that can be used to read TTree values.

As a side note, I am not a TMVA expert but I think TMultiLayerPerceptron is deprecated. See the TMVA tutorials here (or in your ROOT installation folder $ROOTSYS/tutorials/tmva) for examples of current supervised learning algorithms.

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