What happens if a nonprovisional patent application is filed without all required fees?

If a nonprovisional patent application is filed without all required fees, the USPTO will send a notice to the applicant. According to the MPEP:

Filing dates are accorded to nonprovisional applications filed under 37 CFR 1.53(b) submitted without the… required fees (basic filing fee, and search and examination fees (for applications filed on or after December 8, 2004))… In such cases, a notice is mailed by OPAP requiring the appropriate fees… accompanied by a surcharge (37 CFR 1.16(f)).

The applicant will be given a time period (usually two months) to pay the missing fees and surcharge to avoid abandonment of the application.