I don't know that I have a great answer for your question, but I can give you a few ideas that might help. My first suggestion would be to try cleaning (scrubbing with a good brush) with a few different solvents. Start with regular soap and water, then on to acetone, and finally an alcohol (maybe methanol, ethanol or isopropyl alcohol). If you have access to a sonicator, using that would help too. If you have other volatile solvents that you would like to try, they can't hurt either. After you have finished with the alcohol wash, I would put the bottle in an oven to heat for an hour or two at ~120 degrees C. This should be enough to evaporate off any solvent still left.
This is a relatively mild cleaning process that should get rid of most organic compounds. However, if you are not satisfied with that, I would try using a piranha solution to clean them. Piranha is a 3:1 by volume mixture of concentrated sulfuric acid (14 Molar) to 30% hydrogen peroxide. This mixture is an extremely good oxidizing agent, and will get rid of most anything in the bottles. However, it is fairly dangerous. Also, it should only be used in glass bottles, as it will react with some plastics, and with metals. Also, be careful when making the solution, as it is an exothermic reaction and get very hot. (Also, do not use "fuming" sulfuric acid, as this causes the process to be extremely exothermic.) I would typically soak something in a piranha solution for a few hours.
A third option would be to use a base bath. This is typically made by adding sodium hydroxide (NaOH) pellets to isopropyl alcohol (or other alcohol solvent) until it is saturated. Let the bottle sit in the bath submerged overnight and wash thoroughly with water after you take it out. Again there are some dangers as NaOH is a good base so gloves should be work and contact avoided. This might be a better option than the piranha, as it is a little less dangerous.
If you have any questions, or more information about what size/material the bottles are or what you want to use them for after I might be able to offer more help.
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