IRFB3006 vs IRLB3036

I'm about to replace the FETs in a 6-FET controller to create a small but powerful (efficient) controller for a 48V system. My choice of transistors has fallen on either the IRFB3006 or the IRLB3036. As far as i can see the later is both cheaper, has lower gate charge and lower Rds-on but it's logic level. Do this make any difference? They have the same thermal properties but the IRFB3006 seems to have better reverse diode characteristics.

Which of the should i use?

You should use the 3006. The logic-level 3036 will be more susceptible to bad effects like dv/dt-induced turn on. The slight difference in Rdson is not worth the potential for bad things to happen.

Thank you, i guessed that there was something like that to take into consideration.

Another question on the same topic. Has anyone tried Kapton tape as insulator when mounting the transistors against the heatsink?

I have not personally, but it should be a good material for the job. Use the thinnest tape you can get and be sure to use some thermal grease on the FET side.

I've read somewhere that you could use solvent to remove the glue and then use thermal grease on both sides. Perhaps worth a try.

Use KaptonMT instead of the regular kapton (much better thermal conductivity), and try to avoid the pre-adhesive types if you really want maximum performance (just use minimal thermal grease on both sides as LHelge suggests above).