I set a print and forgot to turn on the fan on my E3D. Came back a minute later, the heatsink and extruder were hot to the touch, and the PTFE bowden tube melted inside the cold side and heatbreak. I was able to separate the heatbreak and cold side from the rest of the printer, now how do I clean out all that melted PLA and PTFE in the heatbreak and cold side? Someone suggested burning PLA for cleaning nozzles, but I don't know about doing that to the heatbreak and cold side.

PTFE won't melt at PLA temperatures, even if the whole cold end gets up to nozzle temperature. You may have some melted PLA backed up into the heat break but there shouldn't be any damage to the liner.

What James said. PTFE deformes easily at 250°C, but it will only melt above 320°C. So if it realy melted you have a serious temperature control problem.
Do you have a photo of the molten parts?
Cleaning PLA can be difficult, since it does not dissolve easily. Burning metal parts out can work, though you should only do that outside.
DO NOT burn it out if there is any chance that PTFE is in the mix. Burning PTFE will release toxic chemicals.

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Is it Bowden or direct drive?