Then allow Him to deal with them.

John 1:46, "And Nathanael said unto him, Can there any good thing come out of Nazareth? Philip saith unto him, Come and see."

 

JOHN 1:43-51

 Jesus Calls Philip and Nathanael

43 qThe next day Jesus decided rto go to Galilee. He found Philip and said to him, “Follow me.” 44 Now sPhilip was from Bethsaida, the city of Andrew and Peter. 45 Philip found tNathanael and said to him, “We have found him of whom uMoses in the Law and also the prophets wrote, Jesus vof Nazareth, wthe son of Joseph.” 46 Nathanael said to him, x“Can anything good come out of Nazareth?” Philip said to him, “Come and see.” 47 Jesus saw Nathanael coming toward him and said of him, “Behold, yan Israelite indeed, zin whom there is no deceit!” 48 Nathanael said to him, “How ado you know me?” Jesus answered him, “Before Philip called you, when you were under the fig tree, I saw you.” 49 Nathanael answered him, b“Rabbi, cyou are the Son of God! You are the dKing of Israel!” 50 Jesus answered him, “Because I said to you, ‘I saw you under the fig tree,’ do you believe? You will see greater things than these.” 51 And he said to him, “Truly, truly, I say to you,13 you will see eheaven opened, and fthe angels of God ascending and descending on gthe Son of Man.”

 

** footnotes

q	Jn 1:35 Jn 2:1
r	Jn 1:28
s	Jn 12:21
t	Jn 21:2
u	Lk 16:16 Lk 24:27
v	Mt 2:23
w	Jn 6:42 Lk 3:23
x	Jn 7:41 Jn 7:52
y	Ps 73:1 Ro 9:4 Ro 9:6
z	Ps 32:2 Zep 3:13 Re 14:5
a	Jn 2:24 Jn 2:25
b	Jn 1:38
c	Jn 6:69 Jn 11:27 Jn 20:28
d	Jn 12:13 Zep 3:15 Mt 27:11 Mt 27:42 Zec 9:9
13	The Greek for you is plural; twice in this verse
e	Eze 1:1 Mt 3:16 Lk 3:21
f	Ge 28:12
g	Da 7:13

 

Nathanael suffered from a skepticism that afflicts many people today.

However, it is to his credit that he came to the Lord and gave Him a chance to prove who He was.
We can only speculate what it was that Jesus saw Nathanael doing under that fig tree (v. 50), but it is very clear that it was something that proved beyond a doubt that Jesus was the Christ.

Jesus didn't rebuke Nathanael for his doubts, instead he removed them. The Lord has an answer for every doubt that we have. We need to be without guile before the Lord as Nathanael was (v. 47) and come to Him when we are plagued with doubts instead of running from Him or avoiding Him.  Go to Him with clean hands and a pure heart!

Jesus knows our frame. He remembers that we are but dust (Ps. 103:14).

 For He Himself knows our frame; He is mindful that we are but dust. 
*** 

Adam Clarke Commentary

For he knows our frame - יצרנו yitsrenu, "our formation;" the manner in which we are constructed, and the materials of which we are made. He knows we cannot contend with him, and if he uses his power against us, we must be crushed to destruction. 
In all his conduct towards us he considers the frailty of our nature, the untowardness of our circumstances, the strength and subtlety of temptation, and the sure party (till the heart is renewed) that the tempter has within us. Though all these things are against us, yet it must ever be said, whatever use we make of it, "the grace of God is sufficient for us." But alas! alas! who makes use of that sufficient grace? Here, then, is cause for condemnation. 
But, O amazing mercy! if any man sin, we have an advocate with the Father, Jesus Christ the righteous. And like as a father pitieth his children, so the Lord pitieth them that fear him; for he knows our frame, he remembers that we are but dust. The man who can say, in the face of these Scriptures, Let us sin that grace may abound, is a brute and demon, who has neither lot nor part in this thing.

 It is not a sin to doubt, but it becomes sin if we harbor those doubts. We should do as Nathanael did and bring our doubts to the Lord.

Then allow Him to deal with them.