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  1. testmat = {{0, 1, 3}, {2, 0, 0}, {2, 4, 1}};
  2. ReplacePart[testmat, {i_, i_} -> $MachineEpsilon /; # <= 0 &]
  3.  
  4. ReplacePart[testmat, Position[testmat, # <= 0 &]-> $MachineEpsilon]
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