You can't if you use the same variable for each reader instance: you need to use a separate reader instance for each reader that you instantiate:
$objReader1 = PHPExcel_IOFactory::createReader("Excel5");
$objPHPExcelShip = $objReader1->load("Ship to mapping.xls");
$objReader2 = PHPExcel_IOFactory::createReader("Excel5");
$objPHPExcelMat = $objReader2->load("Material Mapping.xls");
or (at least) instantiate a new reader for each file as you load it
$objReader = PHPExcel_IOFactory::createReader("Excel5");
$objPHPExcelShip = $objReader->load("Ship to mapping.xls");
$objReader = PHPExcel_IOFactory::createReader("Excel5");
$objPHPExcelMat = $objReader->load("Material Mapping.xls");