It work good now. If it is of any help for someone:
*---------
string inputfilename="molfiles/*.mol";
vector <string> inputfiles;
DLHandler::findFiles(inputfiles,inputfilename);
string filename="test.sdf";
vector<string> outputfiles;
outputfiles.push_back(filename);
OBConversion conv;
conv.SetInAndOutFormats("mol","sdf");
filename="test.sdf";
conv.AddOption("gen3D",conv.GENOPTIONS);
conv.FullConvert(inputfiles, filename,outputfiles);
--------*
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