Where can I find Master Ore?

There are 4 Master Ores in the game. Bringing 2 to each Blacksmith will upgrade your sword (First in Hyrule, then in Lorule)

• Lorule Cemetary Dungeon: Enter the Lorule Cemetary through the crack in the Sanctuary. Lift the big rock in the top right corner of the cemetary, then complete the dungeon. The Master Ore is in a big chest at the end. Requires the Titan's Mitts.
• Skull Woods Dungeon: After reaching the 2nd eyeball near the end of the dungeon you’ll see a large chest on a very narrow platform. Merge with the wall ad move towards the platform and open the chest for a Master Ore.
• Thieves’ Hideout: After lowering the water level with the Thief Girl, make your way to the two floor switches on the bottom-left of the room to reveal a long corridor with red rupees and a big chest at the end containing Master Ore.
• Dark Palace: On the top floor with the 6 windows, place a bomb by the lower switch and quickly merge with the top wall’s upper-half with the Boss’s face on it. You’ll go into a room with a large chest containing a piece of Master Ore.

Source: http://www.zeldainformer.com/walkthrough/page/collectibles-guide