T-Bills are discounted instruments there is no accrued interest and nothing to adjust/deduct. Your income in Box 3 should reflect the difference between redemption and purchase prices.
Since you're talking about prices I don't think you mean a Treasury Note with coupons and accrued interest related to a coupon payment in Box 3 .... but if you do then check the "I need to adjust the interest reported on my form" after the 1099 entry screen and follow the on-screen instructions to enter the adjustment.
Note as per the guidance - The adjustment amount entered here will be allocated among the different types of interest reported on this 1099-INT. To apply this adjustment to a specific type of interest, create a separate 1099-INT for each type of interest income, and then enter the adjustment amount applicable to only that type of interest.
