3.25.
From the problem, we can let
C1:m+9x2+my2=1,C2:9−mx2−my2=1,
where 0<m<9.
Let the intersection point be P(x0,y0). Then, since point P lies on C1 and C2, we have m+9x02+9−mx02=2, which simplifies to x02=9−9m2.
Thus, y02=9m2, where x02,y02=0,9.
Therefore, x02+y02=9.
From the sketch (omitted), it is known that there are 25 lattice points within the enclosed region.