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After I've checked the pinout of these 2 device,I found 3C40 use a lot of"VCCINT &GND"in stead of 3C16's "IO",could I design a compatible PCB layout(NC or OUT) for both 2?Any one have the experience on it?
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Yes, you can.
You have to connect the power for the EP3C40 device and set the migration devices in Quartus II to EP3C16 and EP3C40. This implies that you only have the IO pins in the EP3C40 available for User I/O (Quartus II will only use those). You als may want to make sure that in Assignments->Device->Device and Pin Options->Unused Pins you select 'As input -tri-stated with weak pull-up'- Mark as New
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Thanks josyb,your answer really help me:)

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