Helical Tomotherapy, Fludarabine Phosphate, and Melphalan Followed By Allo-HSCT in Hematological Malignancies

Inclusion Criteria: * Recipient, or recipient's parents, or recipient's legal guardians must have signed a voluntary, informed consent in accordance with institutional and federal guidelines * Must have histopathologically confirmed diagnosis in one of the followed categories: * AML * MDS with intermediate or high-risk disease * ALL * Children and adults at any age with significant morbidity, as determined by the primary bone marrow transplant (BMT) doctor (MD), and approved by the principal investigator (PI) * Able to lie supine in a full body cast for approximately 30 minutes, the anticipated duration of each treatment session; for younger patients deep conscious sedation may be required * Performance status evaluated by Zubrod or Karnofsky (KPS) Performance Scales in patients \> 16 years or Lanksy Performance Scale in children =\< 16 years must have a score \>= 70% * Adequate cardiac function: cardiac ejection fraction \> 50% by multi gated acquisition scan (MUGA) scan and/or by echocardiogram * Adequate pulmonary function: adults (older than 16 years): diffusing capacity of carbon monoxide (DLCO) \> 50%; for young children in whom pulmonary function tests (PFT) are not applicable: assessment by a pediatrician or pulmonary consult * Adequate renal function as demonstrated by: creatinine clearance or glomerular filtration rate (GFR) \> 60 cc/min (24 hour urine collection) * Serum glutamic oxaloacetic transaminase (SGOT) and serum glutamic pyruvic transaminase (SGPT) =\< 5.0 times the institutional upper limits of normal * Patients must have less than 15% peripheral blasts * Pre-treatment tests must have been preformed within 30 days prior to initiation of high-dose chemotherapy * No other medical and/or psychosocial problems, which in the opinion of the primary physician or principle investigator would place the patient at unacceptable risk from this regimen Exclusion Criteria: * Patients with Acute Undifferentiated Leukemia (AUL), i.e. no lymphoid or myeloid markers * Previous radiation therapy to more than 20% of bone marrow containing areas, or to any area exceeding 2000 cGy * Patients with Fanconi Anemia * Major medical or psychiatric disorders that would seriously compromise patient tolerance of this regimen * Human immunodeficiency virus (HIV) infection * Evidence of Hepatitis B or C infection or evidence of cirrhosis * Uncontrolled viral, bacterial or fungal infection * Patients with recent (within 4 weeks) serious viral, fungal, or bacterial infection are excluded * Patients with radiographic changes indicating pulmonary disease, including but not limited to: pulmonary nodules, infiltrates, pleural effusion are excluded unless cleared by pulmonary biopsy showing no evidence for active pulmonary disease