I am possibly getting a problem with variation in performance between batches of boards that contain one area which is very current sensitive (to sub nanoamp). Could it be due to manufacturing residue or the board being inadequately washed? If the latter, how would I go about washing the board to check?
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1Isopropyl alcohol (aka Isopropanol, rubbing alcohol, or PCB cleaner). Soak it, then scrub it with a toothbrush. – Majenko Jul 17 '14 at 13:34
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1And then perhaps you could also apply a conformal coating after (mild!) baking to remove moisture. – carveone Jul 17 '14 at 13:39
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80-100°C for 24 hours? That's the a commonly recommended baking time for most moisture sensitive components I have seen, but that is usually more to avoid problems during reflow. – Majenko Jul 17 '14 at 13:41
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What about ultrasonic bath? – Jul 17 '14 at 13:43
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Not sure as I've never had to do it after manufacture. I don't know to what extent moisture ingress would cause current leakage. I used to spray my home-made boards though, just to stop them tarnishing. – carveone Jul 17 '14 at 13:44
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What does the layout look like? – Matt Young Jul 17 '14 at 13:49
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This is a two layer surface mount board, medium density with typically 0805 passives and a LQFP64 processor with 0.2mm pin spacing – Jul 17 '14 at 13:51
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I assume you mean 0.2mm space between pads, the pin pitch can't be anywhere near that narrow. – Spehro Pefhany Jul 17 '14 at 14:22
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Nasty carcinogenic through skin liver poison (they tell) me once used with abandon by dry-cleaners -> Carbon Tetra Chloride, usually does wonders as a final clean. Use after all else fails. Used sensibly it seems to be "safe enough" [tm]. – Russell McMahon Jul 17 '14 at 14:29
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1Guard rings, got, you have? – Russell McMahon Jul 17 '14 at 14:30
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@DirkBruere Related thread: [Cleaning circuit boards for high impedance](http://electronics.stackexchange.com/q/27679/7036) – Nick Alexeev Jul 17 '14 at 23:10
2 Answers
My guess would be the solder flux. Rosin based fluxes are great and I've never had any problems. The water soluble, no-clean and other fluxes have given me no end of headache.
You might ask whoever is making your boards about the flux, maybe you can try a different one.
As far as cleaning, I've only had mixed results. Once the flux gets in there it can get under surface mount components and it's hard to get out. And what to clean with? That would depend on what the flux is. For a water based flux try hot soapy water, there are lots of stories about putting PCB's in a dishwasher for cleaning, but I've never tried this. If it's a "no clean" flux then I'd contact the manufacturer and see if they have a recommendation on what could be used to clean it.

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+1 This is almost surely the answer. No clean flux leaves a fairly conductive residue (when you care about pA) that is very difficult to remove except by physically scrubbing it with relatively harsh solvents. – Spehro Pefhany Jul 17 '14 at 14:21
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Beware that Rosin based fluxes will also stain your manufactured boards. When dealing with sub nA leakage currents *any* kind of dirt and/or moisture can spoil your desired outcome. – jose.angel.jimenez Dec 09 '16 at 14:51
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+1 for remarking that cleaning is not a silver bullet solution and also for "advertising" the "dishwasher" cleaning method. – jose.angel.jimenez Dec 09 '16 at 14:52
If you truly are going to pA level inputs then you are subject to many sources of leakage. You primary solution will be to use a driven guard ring to reduce the leakage currents. Hereis an excellent answer from earlier.
For extremely low levels sometime the inputs are put of posts of teflon.
At these levels even the package matters, normal epoxy packages don't work because of leakage. But there are special formulations of plastic packages that do.
The TLDR version: Washing isn't going to solve your problems if you haven't accounted for stray leakage in your design.

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+1 This should be the accepted answer. Appropriate design including guard rings is the first approach. Then, you have also to take care about cleaning as a secondary issue that can risk your targeted specs/reliability. – jose.angel.jimenez Dec 09 '16 at 14:55