This preset is no longer necessary as the function that it performed can now be achieved natively.

Instead of es2015-native-modules please use es2015 with { "modules": false } option:

presets: [
  ["es2015", { "modules": false }]
]

• babel-plugin-transform-es2015-modules-commonjs

– A preset without transform-es2015-modules-commonjs would help with tree-shaking when using Babel 6 and webpack 2

Tree-shaking with webpack 2 and Babel 6

$ npm install --save-dev babel-preset-es2015-native-modules

.babelrc

{
  "presets": ["es2015-native-modules"]
}

$ babel script.js --presets es2015-native-modules

require("babel-core").transform("code", {
  presets: ["es2015-native-modules"]
});