Yes, if the table already exists then add an INSERT INTO command below the CTE declaration above the SELECT.
If the table doesnt exist, add the INTO clause above the FROM.
WITH rows AS (SELECT *, row_number() OVER (ORDER BY emppin, trxdate) AS rownum
FROM rawtrx)
INSERT INTO atable (col1, col2,.................)
SELECT *, rowsMinusOne.trxtime AS trxtimeIN, ISNULL(rows.trxtime, 1) AS trxtimeOUT
FROM rows AS rowsMinusOne LEFT OUTER JOIN
rows ON rows.rownum = rowsMinusOne.rownum + 1 AND rows.emppin
WITH rows AS (SELECT *, row_number() OVER (ORDER BY emppin, trxdate) AS rownum
FROM rawtrx)
SELECT *, rowsMinusOne.trxtime AS trxtimeIN, ISNULL(rows.trxtime, 1) AS trxtimeOUT
INTO atable
FROM rows AS rowsMinusOne LEFT OUTER JOIN
rows ON rows.rownum = rowsMinusOne.rownum + 1 AND rows.emppin