You can alter a molecule by directly editing its source in the Edit Source dialog window that can be reached from the Edit menu.
The dialog window provides standard clipboard operations.You can view and edit the source in any of the supported file formats.

You can also convert it to Java String which allows easy integration of the structure to a custom Java application code.

To change the format of the source, simply select one from the View Menu.

If there are more than one molecule on the canvas, setting View as multiple molecules in the View Menu causes each molecule to appear in a separate block in the source.

This feature works only in those cases where the selected format is able to handle multiple fragments.

After editing the source text, you can send the structure back to the MarvinSketch canvas by invoking File > Import As, and pressing Import on the appearing dialog window.

This will close the Edit Source dialog window.