If you want to merge a bunch of root TTree's, try the following

> root -q -b merge.C

  where merge.C:

void merge() {
  TChain *chain = new TChain("Global");
  chain->Add("file1.root");
  chain->Add("file2.root");
  chain->Add("file3.root");
  chain->Merge("merged.root");
}

(This example works for RECO_ANALYZE root tuples.)