Is there a utility to replace one block type with another within a region?

I'd like to be able to select a region (either with a graphical utility or command line) and be able to switch one block type with another, e.g. change all cobblestone in the region to stone. Does a program/mod exist that can do this?

As of 1.8, this can be done in vanilla with the /fill command. It can be done using command blocks or typing it straight into the chat.

For example, to change cobblestone to stone:

1.8 to 1.12:

/fill <x1> <y1> <z1> <x2> <y2> <z2> stone 0 replace cobblestone

1.13+:

/fill <x1> <y1> <z1> <x2> <y2> <z2> stone replace cobblestone

Change <x1> <y1> <z1> to the coordinates of one corner of the rectangular area, and <x2> <y2> <z2> with the coordinates of the opposite corner.

WorldEdit has such a command after selecting the area type

//replace [old block] [new block]

This will turn all of the first block from the area into the second block.