1. Capture the squirrel.
You must first put out a squirrel trap. The two best types of squirrel traps are the paw locker and the peanut triggered glock. These are very common traps, and I expect you to know them, so I won't go into detail here. If you want the squirrel to still be alive you should stick with the paw locker.

2. Prepare the microwave.
If you want to avoid a messy clean up, cover every surface of the microwave in either duct tape or aluminum foil. After the squirrel is microwaved, you can simply remove the tape or foil, and the microwave will be as clean as when you started.

3. Microwave it.
Place the squirrel in the microwave. You want to microwave on high until you can't see the whites of it's eyes. (Fun fact: If properly done, you won't be able to see it's eyes because they should have exploded.) This might take from 2-7 minutes, depending on the power of the microwave and the might of the squirrel.

4. Proper disposal.
After you are done with your warm squirrel carcass, you want to cover it in wood glue and pose it in a natural shape in a nearby tree. This prevents anyone from realizing it is dead. Make sure to remove the tape/foil from the inside of your microwave.

And there you have it! A simple guide to microwaving squirrels.

The effects of whole body microwave exposure on the central nervous system (CNS) of the rat were investigated. Rats weighing from 250 to 320 g were exposed for 1 h to whole body microwave with a frequency of 2450 MHz at power densities of 5 and 10 mW·cm−2 at an ambient temperature of 21–23°C. The rectal temperatures of the rats were measured just before and after microwave exposure and mono-amines and their metabolites in various discrete brain regions were determined after microwave exposure. Microwave exposure at power densities of 5 and 10 mW·cm−2 increased the mean rectal temperature by 2.3°C and 3.4°C, respectively. The noradrenaline content in the hypothalamus was significantly reduced after microwave exposure at a power density of 10 mW·cm−2. There were no differences in the dopamine (DA) content of any region of the brain between microwave exposed rats and control rats. The dihydroxyphenyl acetic acid (DOPAC) content, the main metabolite of DA, was significantly increased in the pons plus medulla oblongata only at a power density of 10 mW·cm−2. The DA turnover rates, the DOPAC:DA ratio, in the striatum and cerebral cortex were significantly increased only at a power density of 10 mW·cm−2 The serotonin (5-hydroxytryptamine, 5-HT) content in all regions of the brain of microwave exposed rats was not different from that of the control rats. The 5-hydroxyindoleacetic acid (5-HIAA) content in the cerebral cortex of microwave exposed rats was significantly increased at power densities of 5 and 10 mW·cm−2. The 5-HT turnover rates and the 5-HIAA:5-HT ratio were significantly increased in the cerebral cortex at a power density of 5 mW·cm−2. Significant increases in the 5-HT turnover rate were observed in the pons plus medulla oblongata and hypopthalamus at a power density of 10 mW·cm−2. These results indicated that whole body microwave exposure with a frequency of 2450 MHz at power densities of 5 and 10 mW·cm−2 affected the function of mono-aminergic neurons in the rat brain. It would seem that the effects of whole body microwave exposure on the CNS can be attributed to the hyperthermia characteristic of microwave exposure, although the direct effects of microwave irradiation on the CNS cannot be completely discarded.

Inaba, R., Shishido, Ki., Okada, A. et al. Effects of whole body microwave exposure on the rat brain contents of biogenic amines. Europ. J. Appl. Physiol. 65, 124–128 (1992). https://doi.org/10.1007/BF00705068